| Previous changeset 20:4dbbf92ff30a (2026-05-15) |
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Commit message:
planemo upload commit 24ade7c48613defc1061058737056f0bc64e7709 |
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modified:
Dockerfile job_conf.yml misc/bioconda-recipes-seqsero2s-meta.yml patch_stringmlst.sh seqsero2S.xml tool-data/all_fasta.loc.sample |
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removed:
SeqSero2S/LICENSE SeqSero2S/MANIFEST.in SeqSero2S/README.md SeqSero2S/bin/Initial_Conditions_SS2.py SeqSero2S/bin/Initial_Conditions_SS2S.py SeqSero2S/bin/SeqSero2S.py SeqSero2S/bin/SeqSero2_update_kmer_database.py SeqSero2S/bin/deinterleave_fastq.sh SeqSero2S/seqsero2s_db/H_and_O_and_specific_genes.fasta SeqSero2S/seqsero2s_db/antigens.pickle SeqSero2S/seqsero2s_db/invA_mers_dict SeqSero2S/seqsero2s_db/kmer/salmonella.log SeqSero2S/seqsero2s_db/kmer/salmonella_35.txt SeqSero2S/seqsero2s_db/kmer/salmonella_aroC.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_config.txt SeqSero2S/seqsero2s_db/kmer/salmonella_dnaN.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_hemD.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_hisD.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_profile.txt SeqSero2S/seqsero2s_db/kmer/salmonella_purE.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_sucA.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_thrA.tfa SeqSero2S/seqsero2s_db/kmer/salmonella_weight.txt SeqSero2S/seqsero2s_db/mlst.pickle SeqSero2S/seqsero2s_db/special.pickle SeqSero2S/setup.py |
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| diff -r 4dbbf92ff30a -r 6041d8f4eeeb Dockerfile --- a/Dockerfile Fri May 15 17:55:16 2026 +0000 +++ b/Dockerfile Fri May 15 19:51:16 2026 +0000 |
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| b'@@ -1,138 +1,138 @@\n-# Multi-stage Dockerfile for SeqSero2S\r\n-# Default build: docker build -t seqsero2s:latest .\r\n-# Test build: docker build --target test -t seqsero2s:test .\r\n-\r\n-# ============================================================================\r\n-# Stage 1: Base image with mambaforge for faster dependency resolution\r\n-# ============================================================================\r\n-FROM condaforge/mambaforge:latest AS base\r\n-\r\n-LABEL maintainer="SeqSero2S Maintainers"\r\n-LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"\r\n-\r\n-# Set environment variables to reduce conda output and ensure non-interactive\r\n-# Disable SSL verification for VPN environments\r\n-ENV CONDA_ALWAYS_YES=true \\\r\n- CONDA_AUTO_UPDATE_CONDA=false \\\r\n- DEBIAN_FRONTEND=noninteractive\r\n-\r\n-# Configure conda to skip SSL verification\r\n-RUN conda config --set ssl_verify false\r\n-\r\n-# ============================================================================\r\n-# Stage 2: Builder - Install all dependencies and SeqSero2S\r\n-# ============================================================================\r\n-FROM base AS builder\r\n-\r\n-# Update base packages and install build essentials\r\n-RUN apt-get update && \\\r\n- apt-get install -y --no-install-recommends \\\r\n- wget \\\r\n- ca-certificates \\\r\n- bash \\\r\n- && apt-get clean && \\\r\n- rm -rf /var/lib/apt/lists/*\r\n-\r\n-# Create conda environment with all dependencies\r\n-# Using mamba for faster dependency resolution\r\n-RUN mamba create -n seqsero2s -c conda-forge -c bioconda \\\r\n- python>=3 \\\r\n- pip \\\r\n- setuptools \\\r\n- blast>=2.2 \\\r\n- zstd \\\r\n- samtools \\\r\n- bedtools>=2.17 \\\r\n- sra-tools>=2.8 \\\r\n- spades>=3.9 \\\r\n- salmid \\\r\n- bwa>=0.7 \\\r\n- seqtk>=1.3 \\\r\n- stringmlst>=0.6 \\\r\n- mlst>=2.32.2 \\\r\n- perl-list-moreutils \\\r\n- && mamba clean -afy\r\n-\r\n-# Install SeqSero2S from local fork\r\n-WORKDIR /tmp/build/SeqSero2S\r\n-\r\n-# Copy the current build context (the cloned source code) into the container.\r\n-COPY . .\r\n-\r\n-# Install SeqSero2S\r\n-RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir\r\n-\r\n-# Apply the stringMLST.py patch inline using \'sed\'.\r\n-# This exactly replicates the original python patch script by commenting out the old line and adding the new one.\r\n-RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \\\r\n- sed -i \'s| log = dbPrefix+\'\\\'\'.log\'\\\'\'| # log = dbPrefix+\'\\\'\'.log\'\\\'\'\\n log = os.path.join(os.getcwd(), "kmer.log")|g\' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \\\r\n- echo "PATCHED: stringMLST.py log path fixed"; \\\r\n- else \\\r\n- echo "SKIP: stringMLST.py not found"; \\\r\n- fi\r\n-\r\n-# ============================================================================\r\n-# Stage 3: Test image - runs validation tests\r\n-# ============================================================================\r\n-FROM builder AS test\r\n-\r\n-# Create test directory\r\n-WORKDIR /test\r\n-\r\n-# Run test commands from the conda recipe\r\n-RUN echo "Running SeqSero2S tests..." && \\\r\n- /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \\\r\n- echo "SeqSero2S.py -h: PASSED" && \\\r\n- /opt/conda/envs/seqsero2s/bin/blastn -help && \\\r\n- echo "blastn -help: PASSED" && \\\r\n- /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \\\r\n- echo "SalmID.py -h: PASSED" && \\\r\n- /opt/conda/envs/seqsero2s/bin/mlst -h && \\\r\n- echo "mlst -h: PASSED" && \\\r\n- echo "All tests completed successfully!"\r\n-\r\n-# Default command shows test results\r\n-CMD ["echo", "All SeqSero2S tests passed successfully!"]\r\n-\r\n-# ============================================================================\r\n-# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)\r\n-# ============================================================================\r\n-FROM condaforge/mambaforge:latest AS dist\r\n-\r\n-# Copy conda environment from builder\r\n-C'..b'&& \\\n+ apt-get install -y --no-install-recommends \\\n+ wget \\\n+ ca-certificates \\\n+ bash \\\n+ && apt-get clean && \\\n+ rm -rf /var/lib/apt/lists/*\n+\n+# Create conda environment with all dependencies\n+# Using mamba for faster dependency resolution\n+RUN mamba create -n seqsero2s -c conda-forge -c bioconda \\\n+ python>=3 \\\n+ pip \\\n+ setuptools \\\n+ blast>=2.2 \\\n+ zstd \\\n+ samtools \\\n+ bedtools>=2.17 \\\n+ sra-tools>=2.8 \\\n+ spades>=3.9 \\\n+ salmid \\\n+ bwa>=0.7 \\\n+ seqtk>=1.3 \\\n+ stringmlst>=0.6 \\\n+ mlst>=2.32 \\\n+ perl-list-moreutils \\\n+ && mamba clean -afy\n+\n+# Install SeqSero2S from local fork\n+WORKDIR /tmp/build/SeqSero2S\n+\n+# Copy the current build context (the cloned source code) into the container.\n+COPY . .\n+\n+# Install SeqSero2S\n+RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir\n+\n+# Apply the stringMLST.py patch inline using \'sed\'.\n+# This exactly replicates the original python patch script by commenting out the old line and adding the new one.\n+RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \\\n+ sed -i \'s| log = dbPrefix+\'\\\'\'.log\'\\\'\'| # log = dbPrefix+\'\\\'\'.log\'\\\'\'\\n log = os.path.join(os.getcwd(), "kmer.log")|g\' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \\\n+ echo "PATCHED: stringMLST.py log path fixed"; \\\n+ else \\\n+ echo "SKIP: stringMLST.py not found"; \\\n+ fi\n+\n+# ============================================================================\n+# Stage 3: Test image - runs validation tests\n+# ============================================================================\n+FROM builder AS test\n+\n+# Create test directory\n+WORKDIR /test\n+\n+# Run test commands from the conda recipe\n+RUN echo "Running SeqSero2S tests..." && \\\n+ /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \\\n+ echo "SeqSero2S.py -h: PASSED" && \\\n+ /opt/conda/envs/seqsero2s/bin/blastn -help && \\\n+ echo "blastn -help: PASSED" && \\\n+ /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \\\n+ echo "SalmID.py -h: PASSED" && \\\n+ /opt/conda/envs/seqsero2s/bin/mlst -h && \\\n+ echo "mlst -h: PASSED" && \\\n+ echo "All tests completed successfully!"\n+\n+# Default command shows test results\n+CMD ["echo", "All SeqSero2S tests passed successfully!"]\n+\n+# ============================================================================\n+# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)\n+# ============================================================================\n+FROM condaforge/mambaforge:latest AS dist\n+\n+# Copy conda environment from builder\n+COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s\n+\n+# Update PATH to use the conda environment\n+ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \\\n+ CONDA_DEFAULT_ENV=seqsero2s \\\n+ CONDA_PREFIX=/opt/conda/envs/seqsero2s\n+\n+# Install minimal runtime dependencies\n+RUN apt-get update && \\\n+ apt-get install -y --no-install-recommends \\\n+ ca-certificates \\\n+ procps \\\n+ && apt-get clean && \\\n+ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*\n+\n+# Create working directory\n+WORKDIR /data\n+\n+# Create non-root user for running the application\n+RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \\\n+ chown -R seqsero2s:seqsero2s /data\n+USER seqsero2s\n+\n+# Add metadata labels\n+LABEL org.opencontainers.image.version="1.1.4" \\\n+ org.opencontainers.image.authors="LSTUGA" \\\n+ org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \\\n+ org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \\\n+ org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \\\n+ org.opencontainers.image.licenses="GPL-2.0-or-later" \\\n+ org.opencontainers.image.title="SeqSero2S" \\\n+ org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"\n+\n+# No entrypoint or command for dist target\n+\n+\n' |
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| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/LICENSE --- a/SeqSero2S/LICENSE Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,342 +0,0 @@\n-NOTE: parties interested in commercial licenses should contact the UGA\xe2\x80\x99s Innovation Gateway (https://research.uga.edu/gateway/).\n-\n-\n-GNU GENERAL PUBLIC LICENSE\n- Version 2, June 1991\n- \n- Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>\n- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\n- Everyone is permitted to copy and distribute verbatim copies\n- of this license document, but changing it is not allowed.\n-\n- Preamble\n-\n- The licenses for most software are designed to take away your\n-freedom to share and change it. By contrast, the GNU General Public\n-License is intended to guarantee your freedom to share and change free\n-software--to make sure the software is free for all its users. This\n-General Public License applies to most of the Free Software\n-Foundation\'s software and to any other program whose authors commit to\n-using it. 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| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/MANIFEST.in --- a/SeqSero2S/MANIFEST.in Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -include LICENSE -include README.md -include MANIFEST.in -include version.py -include setup.py -include seqsero2s_db/antigens.pickle -include seqsero2s_db/H_and_O_and_specific_genes.fasta -include seqsero2s_db/invA_mers_dict -include seqsero2s_db/special.pickle -include seqsero2s_db/mlst.pickle -include seqsero2s_db/kmer/salmonella_35.txt -include seqsero2s_db/kmer/salmonella_aroC.tfa -include seqsero2s_db/kmer/salmonella_config.txt -include seqsero2s_db/kmer/salmonella_dnaN.tfa -include seqsero2s_db/kmer/salmonella_hemD.tfa -include seqsero2s_db/kmer/salmonella_hisD.tfa -include seqsero2s_db/kmer/salmonella.log -include seqsero2s_db/kmer/salmonella_profile.txt -include seqsero2s_db/kmer/salmonella_purE.tfa -include seqsero2s_db/kmer/salmonella_sucA.tfa -include seqsero2s_db/kmer/salmonella_thrA.tfa -include seqsero2s_db/kmer/salmonella_weight.txt -include bin/deinterleave_fastq.sh -include bin/Initial_Conditions_SS2.py -include bin/Initial_Conditions_SS2S.py |
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| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/README.md --- a/SeqSero2S/README.md Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,151 +0,0 @@ -# SeqSero2S - -Salmonella serotype prediction from genome sequencing data. - -Online version: http://www.denglab.info/SeqSero2 - -# Updates since SS2 v1.2.1 -1. Convert the sequences of the following alleles to their reverse complement sequences in the SeqSero2 database. -``` --fliC_b_Wien_CDC_b,d,j__1488\ --fliC_d_from-II-48:d:z6_SRR1168371__1521\ --fliC_a_Salmonella.enterica_from-cdc-Stk2184_other.a__1488 --fliC_l,v_from-Nchanga_SRR1153349__1503 --fliC_l,z13,z28_Salmonella.enterica_from-CDC_2011K-0215_l,v__1506 --fljB_1,7_Salmonella.enterica_from-cdc_Stk1415_1__1521 --fljB_1,5_from-cdc_Stk2184_1__1521 --fljB_1,5_from-Infantis-micro-assembly_SRR1106258_1__1521 --fljB_z6_from-II-48:d:z6_SRR1168371__1503 -``` -2. Delete the following alleles from the SeqSero2 database because of the existence of mutations. -``` --fliC_y_Bareillystr_AOZP01000027_other.y__1508 --fliC_d_Muenchenstr_ARYW01000085_b,d,j__1496 --fliC_d_Muenchenstr_ARYX01000110_b,d,j__1488 --fliC_g,m_Enteritidisstr_ALHD01000038_g,m__1507 --fljB_1,2_Newportstr_AYDZ01000021_1__1510 -``` -2. Add a fliC 1,5,7 allele and a fliC 1,2,7 allele into the SeqSero2 database. -``` --fliC_1,5,7_Salmonella.enterica_from-cdc-Stk1778_1,5,7_1521 --fliC_1,2,7_Salmonella.enterica_from-cdc-Stk2293_1,2,7_1521 -``` -3. Delete the O54 allele -``` --O-54_wbbF__1380 -``` -4. Fixed the bug that caused the misidentification of O9 and O2 by the micro-assembly workflow -5. Update serotype names based on the simplified KWS scheme -6. Remove the 9,46,27 allele -``` --O-9,46,27_partial_wzy__1019 -``` -7. Remove two fljB_1,2 allels -``` --fljB_1,2_from-Brazzaville_SRR2058145_1__1521 --fljB_1,2_Salmonella.enterica_1,4,5,12:i:1,2,7_AY353272_1__1521 -``` -8. Run 7-gene MLST analysis using stringMLST/mlst - -# Introduction -SeqSero2S is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies - -# Dependencies -SeqSero2S has three workflows: - -(A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). - -Allele micro-assembly workflow depends on: - -1. Python 3; -2. Biopython 1.73; -3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); -4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); -5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); -6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); -7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); -8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); -9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID); -10. [stringMLST v0.6.3](https://github.com/jordanlab/stringMLST); - -(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. - -Raw reads k-mer workflow (originally SeqSeroK) depends on: - -1. Python 3; -2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); -3. [mlst v2.22.1](https://github.com/tseemann/mlst). - - -(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow - -# Installation -### Git -Install mlst and stringMLST first -``` -conda install mlst -``` -``` -pip install stringMLST -``` -To install the SeqSero2S git repository locally: -``` -git clone https://github.com/LSTUGA/SeqSero2S.git -cd SeqSero2S -python3 -m pip install --user . -``` - -# Executing the code -Make sure all SeqSero2S and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2S.py to get detailed instructions. - - Usage: SeqSero2S.py - - -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) - - -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore reads (fasta/fastq)) - - -i <file> (/path/to/input/file) - - -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) - - -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) - - -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) - - -c <flag> (if '-c' was flagged, SeqSero2S will only output serotype prediction without the directory containing log files) - - -n <string> (optional, to specify a sample name in the report output) - - -s <flag> (if '-s' was flagged, SeqSero2S will not output header in SeqSero_result.tsv) - - --check <flag> (use '--check' flag to check the required dependencies) - - -v, --version (show program's version number and exit) - - -# Examples -Allele mode: - - # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") - SeqSero2S.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz - -K-mer mode: - - # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") - SeqSero2S.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz - - # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") - SeqSero2S.py -m k -t 4 -i assembly.fasta - -# Output -Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). - - -# Citation -Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. -SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. -**Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) - -Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. -Salmonella serotype determination utilizing high-throughput genome sequencing data. -**J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/bin/Initial_Conditions_SS2.py --- a/SeqSero2S/bin/Initial_Conditions_SS2.py Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,109 +0,0 @@\n-#!/usr/bin/env python\n-\n-subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'VI', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 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'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun']\n-\n-rename_dict={'Nitra': 'Enteritidis',\n- 'Kiel': 'Dublin',\n- 'Koessen': 'Panama',\n- 'Phaliron': 'Kalumburu',\n- 'Istanbul': 'Hadar',\n- 'Haardt': 'Blockley',\n- 'Ferruch': 'Kottbus',\n- 'Sanga': 'Eboko',\n- 'Pakistan': 'Litchfield',\n- 'Bellevue': 'Lezennes',\n- 'Sunnycove': 'Daarle',\n- 'Noya': 'Akanji',\n- 'Virginia': 'Muenchen',\n- 'Djelfa': 'Skansen',\n- 'Konstanz': 'Gatuni',\n- 'Bardo': 'Newport',\n- 'Houston': 'Panama',\n- 'Martonos': 'Finkenwerder',\n- 'Midway': 'Florida',\n- 'Lindern': 'Charity',\n- 'Bahrenfeld': 'Onderstepoort',\n- 'Schalkwijk': 'Moussoro',\n- 'Amberg': 'Boecker',\n- 'Madelia': 'Carrau',\n- 'Soahanina': 'Sundsvall',\n- 'Stafford': 'Poano',\n- 'Chichiri': 'Uzaramo',\n- 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]',\n- 'Hindmarsh':'Bovismorbificans',\n- 'Yovokome': 'Manhattan'}\n-\n- #potential merge for O22 and O23\n- #'Ibadan': 'Mississippi',\n- #'Bracknell': 'Oudwijk',\n- #'Vaertan': 'Ullevi',\n- #'Bahati': 'Durham',\n- #'Wichita': 'Friedenau',\n- #'Diguel': 'Telelkebir',\n- #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5',\n- #'Washington': 'Kintambo',\n- #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39',\n- #'Serenli': 'Winslow',\n- #'Farmsen': 'Poona',\n- #'Durance': 'Ivrysurseine',\n- #'Agoueve': 'Cubana',\n- #'II 13,23:z29:1,5': 'II 13,22:z29:1,5',\n- #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x',\n- #'Picpus': 'Mampong',\n- #'Anna': 'Nimes',\n- #'Fanti': 'Leiden',\n- #'Ried': 'Ajiobo',\n-\n- #potential O68 list\n- #'Djelfa': 'Skansen',\n- #'Korbol': 'Nagoya',\n- #'Sanga': 'Eboko',\n- #'Konstanz': 'Gatuni',\n- #'Presov': 'Shipley',\n- #'Heistopdenberg': 'Bukuru',\n- #'Tounouma': 'Banalia',\n- #'Gaillac': 'Utah',\n- #'Santiago': 'Belem',\n- #'Virginia': 'Muenchen',\n- #'Yovokome': 'Manhattan',\n- #'Portanigra': 'Dunkwa',\n- #'Bardo': 'Newport',\n- #'Ferruch': 'Kottbus',\n- #'Alminko': 'Nanergou',\n- #'Bargny': 'Takoradi',\n- #'Magherafelt': 'Cyprus',\n- #'Haardt': 'Blockley',\n- #'Pakistan': 'Litchfield',\n- #'Yokoe': 'Bassa',\n- #'Noya': 'Akanji',\n- #'Lamphun': 'Giza',\n- #'Tananarive': 'Brunei',\n- #'Inchpark': 'Alagbon',\n- #'Sunnycove': 'Daarle',\n- #'Sindelfingen': 'Benue',\n- #'Phaliron': 'Kalumburu',\n- #'Bazenheid': 'Zerifin',\n- #'Paris': 'Mapo',\n- #'Istanbul': 'Hadar',\n- #'Chomedey': 'Glostrup',\n- #'Wippra': 'Molade',\n- #'Uno': 'Tamale',\n- #'Kolda': 'Yarm',\n- #'Bellevue': 'Lezennes',\n- #'Albany':'Duesseldorf'\n" |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/bin/Initial_Conditions_SS2S.py --- a/SeqSero2S/bin/Initial_Conditions_SS2S.py Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,110 +0,0 @@\n-#!/usr/bin/env python\n-\n-subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'VI', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 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'I', 'I', 'I', 'II', 'I', 'I', 'IIIb', 'I', 'I', 'IIIb', 'IIIb', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'IIIb', 'IIIb', 'IIIb', 'I', 'I', 'I', 'I', 'IIIb', 'IIIb', 'I', 'I', 'I', 'II', 'IIIb', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'IIIb', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'IIIb', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'IV', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'II', 'bongori', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I"..b"0:m,t:z42', 'II 40:z:z42', 'II [1],40:z42:1,6', 'II 43:b:z42', 'II 43:d:z42', 'II 43:z29:z42', 'II 43:z42:[1,5,7]', 'II 44:g,t:z42', 'II [1],44:m,t:z42', 'II 45:z29:z42', 'II 50:l,z28:z42', 'II 50:z42:1,7', 'II 53:d:z42', 'II 57:a:z42', 'II 57:z29:z42', 'II 57:z42:1,6:z53', 'II 3,10:z38:z42', 'II 1,6,14:z42:1,6', 'IIIb 18:(k):z54', 'IIIb 47:l,v:z57', 'IIIb 50:l,v:z57', 'IIIb 38:(k):z55', 'IIIb 21:l,v:z57', 'IIIb 48:k:z57', 'IIIb 59:z10:z57', 'IIIb 42:z57:1,5', 'Aesch', 'IIIb 38:z61:[z53]', 'Oakey', 'Aarhus', 'Franken', 'IIIb 42:z10:z67', 'VI 50:l,v:z67', 'IIIb 53:r:z68', 'Delmenhorst', 'II 3,15:z87:e,n,x,z15', 'VI 6,14:l,v:z88', 'Mygdal', 'II 1,9,12,46,27:a:z6', 'II 1,9,12,46,27:b:z39', 'II 1,9,12,46,27:c:z39', 'II 9,12,46,27:g,t:e,n,x', 'II 1,9,12,46,27:l,z13,z28:z39', 'II 1,9,12,46,27:y:z39', 'II 1,9,12,46,27:z10:1,5', 'II 1,9,12,46,27:z10:e,n,x', 'II 1,9,12,46,27:z10:z39', 'II 1,9,12,46,27:z4,z24:1,5', 'Tonev', 'Winnipeg', 'Rossleben', 'Borreze', 'Uccle', 'Poeseldorf', 'Ochsenwerder', 'Newholland', 'Czernyring', 'Steinwerder', 'Canton', 'Barry', 'Mundubbera', 'Yerba', 'Sendai', 'Abortusequi']\n-\n-rename_dict={\n- 'Nitra': 'Enteritidis',\n- 'Kiel': 'Dublin',\n- 'Koessen': 'Panama',\n- 'Phaliron': 'Kalumburu',\n- 'Istanbul': 'Hadar',\n- 'Haardt': 'Blockley',\n- 'Ferruch': 'Kottbus',\n- 'Eboko': 'Sanga',\n- 'Pakistan': 'Litchfield',\n- 'Bellevue': 'Lezennes',\n- 'Daarle': 'Sunnycove',\n- 'Noya': 'Akanji',\n- 'Virginia': 'Muenchen',\n- 'Skansen': 'Djelfa',\n- 'Konstanz': 'Gatuni',\n- 'Bardo': 'Newport',\n- 'Houston': 'Panama',\n- 'Martonos': 'Finkenwerder',\n- 'Midway': 'Florida',\n- 'Lindern': 'Charity',\n- 'Bahrenfeld': 'Onderstepoort',\n- 'Moussoro': 'Schalkwijk',\n- 'Amberg': 'Boecker',\n- 'Madelia': 'Carrau',\n- 'Soahanina': 'Sundsvall',\n- 'Stafford': 'Poano',\n- 'Chichiri': 'Uzaramo',\n- 'Hindmarsh':'Bovismorbificans',\n- 'Yovokome': 'Manhattan',\n- ## SS2S\n- 'Fulica': 'I 4:a:-',\n- 'Korbol': 'Nagoya',\n- 'Presov': 'Shipley',\n- 'Heistopdenberg': 'Bukuru',\n- 'Tounouma': 'Banalia',\n- 'Gaillac': 'Utah',\n- 'Santiago': 'Belem',\n- 'Portanigra': 'Dunkwa',\n- 'Alminko': 'Nanergou',\n- 'Bargny': 'Takoradi',\n- 'Magherafelt': 'Cyprus',\n- 'Bassa': 'Yokoe',\n- 'Lamphun': 'Giza',\n- 'Brunei': 'Tananarive',\n- 'Inchpark': 'Alagbon',\n- 'Sindelfingen': 'Benue',\n- 'Bazenheid': 'Zerifin',\n- 'Paris': 'Mapo',\n- 'Chomedey': 'Glostrup',\n- 'Wippra': 'Molade',\n- 'Uno': 'Tamale',\n- 'Kolda': 'Yarm',\n- 'Duesseldorf': 'Albany',\n- 'Rosenberg': 'Enteritidis',\n- 'Blegdam': 'Enteritidis',\n- 'Moscow': 'Enteritidis',\n- 'Antarctica': 'Enteritidis',\n- #'Chincol': 'Emek',\n- 'Dessau': 'Senftenberg',\n- 'Naestved': 'Dublin',\n- 'Rostock': 'Dublin',\n- ##update names\n- 'IIIb 6,7:(k):z': 'IIIb 7:k:z',\n- 'IIIb 16:(k):e,n,x,z15': 'IIIb 16:k:e,n,x,z15',\n- 'IIIb 60:i:[e,n,x,z15]': 'IIIb 60:i:e,n,x,z15',\n- 'IIIb 60:i:[z]': 'IIIb 60:i:z',\n- 'IIIb 60:i:[z35]': 'IIIb 60:i:z35',\n- 'II [1],13,22:g,m,t:[1,5]': 'II 13,22:g,m,t:1,5',\n- 'II 6,7:z29:[z42]': 'II 7:z29:-',\n- 'II [1],13,22:g,t:[1,5]': 'II 13,22:g,t:1,5',\n- 'II 16:m,t:[z42]': 'II 16:m,t:-',\n- 'II 17:g,t:[e,n,x,z15]': 'II 17:g,t:e,n,x,z15',\n- 'VI 1,6,14,25:z10:1,(2),7': 'VI 6,14:z10:1,2,7',\n- 'II 13,22:m,t:z42:z39': 'II 13,22:m,t:z39',\n-}\n-\n-#potential merge for O22 and O23\n- #'Ibadan': 'Mississippi',\n- #'Bracknell': 'Oudwijk',\n- #'Vaertan': 'Ullevi',\n- #'Bahati': 'Durham',\n- #'Wichita': 'Friedenau',\n- #'Diguel': 'Telelkebir',\n- #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5',\n- #'Washington': 'Kintambo',\n- #'Winslow': 'Serenli',\n- #'Farmsen': 'Poona',\n- #'Ivrysurseine': 'Durance',\n- #'Agoueve': 'Cubana',\n- #'II [1],13,23:z29:1,5': 'II 13,22:z29:1,5',\n- #'II [1],13,23:z29:e,n,x': 'II 13,22:z29:e,n,x',\n- #'Picpus': 'Mampong',\n- #'Nimes': 'Anna',\n- #'Fanti': 'Leiden',\n- #'Ried': 'Ajiobo',\n" |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/bin/SeqSero2S.py --- a/SeqSero2S/bin/SeqSero2S.py Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1723 +0,0 @@\n-#!/usr/bin/env python3\n-\n-import sys\n-import time\n-import random\n-import os\n-import subprocess\n-import gzip\n-import io\n-import pickle\n-import argparse\n-import itertools\n-import json\n-from distutils.version import LooseVersion\n-from distutils.spawn import find_executable\n-sys.path.insert(1,sys.path[0]+\'/..\')\n-\n-__version__ = "1.1.4"\n-\n-### SeqSero Kmer\n-def parse_args():\n- "Parse the input arguments, use \'-h\' for help."\n- parser = argparse.ArgumentParser(usage=\'SeqSero2S.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\\n\\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\\n\\nContact email:seqsero@gmail.com\\n\\n\')#add "-m <data_type>" in future\n- parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### add \'type=os.path.abspath\' to generate absolute path of input data.\n- parser.add_argument("-t",choices=[\'1\',\'2\',\'3\',\'4\',\'5\'],help="<int>: \'1\' for interleaved paired-end reads, \'2\' for separated paired-end reads, \'3\' for single reads, \'4\' for genome assembly, \'5\' for nanopore reads (fasta/fastq)")\n- parser.add_argument("-b",choices=[\'sam\',\'mem\'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; \'mem\' for mem, \'sam\' for samse/sampe; default=mem; optional; for now we only optimized for default \'mem\' mode")\n- parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1")\n- parser.add_argument("-m",choices=[\'k\',\'a\'],default="a",help="<string>: which workflow to apply, \'a\'(raw reads allele micro-assembly), \'k\'(raw reads and genome assembly k-mer), default=a")\n- parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output")\n- parser.add_argument("-d",help="<string>: optional, to specify an output directory name, if not set, the output directory would be \'SeqSero_result_\'+time stamp+one random number")\n- parser.add_argument("-c",action="store_true",help="<flag>: if \'-c\' was flagged, SeqSero2S will only output serotype prediction without the directory containing log files")\n- parser.add_argument("-s",action="store_true",help="<flag>: if \'-s\' was flagged, SeqSero2S will not output header in SeqSero_result.tsv")\n- parser.add_argument("--phred_offset",choices=[\'33\',\'64\',\'auto\'],default=\'auto\',help="<33|64|auto>: offset for FASTQ file quality scores, default=auto")\n- parser.add_argument("--check",action="store_true",help="<flag>: use \'--check\' flag to check the required dependencies")\n- parser.add_argument(\'-v\', \'--version\', action=\'version\', version=f"%(prog)s {__version__}")\n- return parser.parse_args()\n-\n-### check paths of dependencies\n-check_dependencies = parse_args().check\n-dependencies = [\'bwa\',\'samtools\',\'blastn\',\'fastq-dump\',\'spades.py\',\'bedtools\',\'SalmID.py\',\'mlst\',\'stringMLST.py\']\n-if check_dependencies:\n- for item in dependencies:\n- ext_path = find_executable(item)\n- if ext_path is not None:\n- print ("Using "+item+" - "+ext_path)\n- else:\n- print ("ERROR: can not find "+item+" in PATH")\n- sys.exit()\n-### end of --check\n-\n-def reverse_complement(sequence):\n- complement = {\n- \'A\': \'T\',\n- \'C\': \'G\',\n- \'G\': \'C\',\n- \'T\': \'A\',\n- \'N\': \'N\',\n- \'M\': \'K\',\n- \'R\': \'Y\',\n- \'W\': \'W\',\n- \'S\': \'S\',\n- \'Y\': \'R\',\n- \'K\': \'M\',\n- \'V\': \'B\',\n- \'H\': \'D\',\n- \'D\': \'H\',\n- \'B\': \'V\'\n- }\n- return "".join(complement[base] for base in reversed(sequence))\n-\n-def mlst(assembly):\n- subprocess.check_call("mlst -q --json mlst.json --scheme senterica_achtman_2 "+assembly+" >> data_log.txt 2>&1",shell=True)\n- f = open("mlst.json",\'r\')\n- mlst_result = json.load(f)\n- f.close()\n-'..b'"\\n"+\n- "O antigen prediction:\\t"+O_choice+"\\n"+\n- "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n- "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n- "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n- "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n- "Predicted serotype:\\t"+predict_sero+"\\n"+\n- "Predicted serotype (SeqSero2 v1.3.2):\\t"+predict_sero_ss2+"\\n"+\n- note+star_line+claim+antigen_note+"\\n")#+##\n- tsv_file.write(make_dir+"\\t"+input_file+"\\t"+O_choice+"\\t"+highest_fliC+"\\t"+highest_fljB+"\\t"+subspecies_ID_dir[ssp_pointer]+"\\t"+predict_form+"\\t"+predict_sero+"\\t"+predict_sero_ss2+"\\t"+star_line+claim+antigen_note+"\\t"+st+"\\n")\n- else:\n- new_file.write("Output directory:\\t"+make_dir+"\\n"+\n- "Input files:\\t"+input_file+"\\n"+\n- "O antigen prediction:\\t"+O_choice+"\\n"+\n- "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n- "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n- "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n- "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n- "Predicted serotype:\\t"+subspecies+\' \'+predict_form+"\\n"+ # add serotype output for "N/A" prediction, subspecies\n- "Predicted serotype (SeqSero2 v1.3.2):\\t"+subspecies+\' \'+predict_form_ss2+"\\n"+\n- note+NA_note+star_line+claim+antigen_note+"\\n")#+##\n- tsv_file.write(make_dir+"\\t"+input_file+"\\t"+O_choice+"\\t"+highest_fliC+"\\t"+highest_fljB+"\\t"+subspecies_ID_dir[ssp_pointer]+"\\t"+predict_form+"\\t"+subspecies+\' \'+predict_form+"\\t"+subspecies+\' \'+predict_form_ss2+"\\t"+NA_note+star_line+claim+antigen_note+"\\t"+st+"\\n")\n- ###MLST\n- new_file.write("Sequence type:\\t"+st+"\\n"+\n- "Number of ST"+st+" strains in EnteroBase:\\t"+st_count+"\\n"+\n- "\\n".join([k+":\\t"+v for k,v in sorted_alleles]))\n- ###\n- new_file.close()\n- tsv_file.close()\n- if "N/A" not in predict_sero:\n- print("Output directory:\\t"+make_dir+"\\n"+\n- "Input files:\\t"+input_file+"\\n"+\n- "O antigen prediction:\\t"+O_choice+"\\n"+\n- "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n- "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n- "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n- "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n- "Predicted serotype:\\t"+predict_sero+"\\n"+\n- "Predicted serotype (SeqSero2 v1.3.2):\\t"+predict_sero_ss2+"\\n"+\n- note+star_line+claim+antigen_note+"\\n")#+##\n- else:\n- print("Output directory:\\t"+make_dir+"\\n"+\n- "Input files:\\t"+input_file+"\\n"+\n- "O antigen prediction:\\t"+O_choice+"\\n"+\n- "H1 antigen prediction(fliC):\\t"+highest_fliC+"\\n"+\n- "H2 antigen prediction(fljB):\\t"+highest_fljB+"\\n"+\n- "Predicted identification:\\t"+subspecies_ID_dir[ssp_pointer]+"\\n"+\n- "Predicted antigenic profile:\\t"+predict_form+"\\n"+\n- "Predicted serotype:\\t"+subspecies+\' \'+predict_form+"\\n"+ # add serotype output for "N/A" prediction, subspecies\n- "Predicted serotype (SeqSero2 v1.3.2):\\t"+subspecies+\' \'+predict_form_ss2+"\\n"+\n- note+NA_note+star_line+claim+antigen_note+"\\n")#+##\n- ###MLST\n- print("Sequence type: "+st)\n- print("Number of ST"+st+" strains in EnteroBase: "+st_count)\n- #print("Allele profile...")\n- for k,v in sorted_alleles:\n- print(k+\': \'+v)\n- print(\'\\n\')\n- ###\n-if __name__ == \'__main__\':\n- main()\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/bin/SeqSero2_update_kmer_database.py --- a/SeqSero2S/bin/SeqSero2_update_kmer_database.py Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,113 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import os,subprocess -import pickle - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') - return parser.parse_args() - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - -def multifasta_to_kmers_dict(multifasta): - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) - return lib_dict - -def get_salmid_invA_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/invA_mers_dict', 'rb') - invA_dict = pickle.load(a) - try: - del invA_dict['version'] - except: - pass - return invA_dict - -def get_salmid_rpoB_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/rpoB_mers_dict', 'rb') - rpoB_dict = pickle.load(a) - try: - del rpoB_dict['version'] - except: - pass - return rpoB_dict - -def main(): - args = parse_args() - ex_dir = os.path.dirname(os.path.realpath(__file__)) - lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') - invA_dict=get_salmid_invA_database(ex_dir) - #rpoB_dict=get_salmid_rpoB_database(ex_dir) - lib_dict_new = lib_dict.copy() - #print(len(lib_dict_new)) - lib_dict_new.update(invA_dict) - #print(len(lib_dict_new)) - #lib_dict_new.update(rpoB_dict) - #print(len(lib_dict_new)) - f = open(ex_dir + '/antigens.pickle', "wb") - pickle.dump(lib_dict_new, f) - f.close() - -if __name__ == '__main__': - main() |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/bin/deinterleave_fastq.sh --- a/SeqSero2S/bin/deinterleave_fastq.sh Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,30 +0,0 @@ -#!/bin/bash -# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] -# -# Deinterleaves a FASTQ file of paired reads into two FASTQ -# files specified on the command line. Optionally GZip compresses the output -# FASTQ files using pigz if the 3rd command line argument is the word "compress" -# -# Can deinterleave 100 million paired reads (200 million total -# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) -# -# Latest code: https://gist.github.com/3521724 -# Also see my interleaving script: https://gist.github.com/4544979 -# -# Inspired by Torsten Seemann's blog post: -# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html - -# Set up some defaults -GZIP_OUTPUT=0 -PIGZ_COMPRESSION_THREADS=10 - -# If the third argument is the word "compress" then we'll compress the output using pigz -if [[ $3 == "compress" ]]; then - GZIP_OUTPUT=1 -fi - -if [[ ${GZIP_OUTPUT} == 0 ]]; then - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 -else - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 -fi |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/H_and_O_and_specific_genes.fasta --- a/SeqSero2S/seqsero2s_db/H_and_O_and_specific_genes.fasta Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6923 +0,0 @@\n->fliC_g,m_Enteritidisstr_AKFY01000033_g,m__1506\n-ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC\n-CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT\n-TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT\n-GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC\n-CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG\n-GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG\n-CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA\n-ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG\n-CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA\n-AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT\n-TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA\n-ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT\n-AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA\n-AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG\n-AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA\n-AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC\n-AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG\n-TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG\n-ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT\n->fliC_g,m,s_Montevideostr_AESV01000018_g,m__1506\n-ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC\n-CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT\n-TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC\n-GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC\n-CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG\n-GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG\n-CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA\n-ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG\n-CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA\n-AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT\n-TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA\n-ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT\n-AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA\n-AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG\n-AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT\n-AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC\n-AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG\n-TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG\n-ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT\n->fljB_1,2_Salmonella.enterica_Stanley_AY353267_1__1521\n-ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC\n-CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT\n-TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC\n-GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC\n-TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG\n-GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG\n-AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC\n-AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG\n-GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT'..b'CGGTGACAATGACCGCAAATAAATCAACAGTAACTGGGGCCGG\n-CACAGTTACCAAAAACCAAATTGTAGACGCTGTTACTCCGGCACCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCA\n-ATGCAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGAT\n-GCGGGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAGACTGGTGAGATAAAAGCTAAGAC\n-TGTAAATTATACTGACGCTACTGGTGCAACAAAAACTGGTGCTGTGAAATTTGGCGGCGCGAATGGTAAAACTGAAGTTG\n-TGACTACAGTTGATGGTAATACTTATCAGGCTAGTGATGTGAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGTGAG\n-GCTGTGACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCT\n-GGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAATCTGGGCAATACCGTAAACAACTTGTCTGAAGCGCGTAGCC\n-GTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTT\n-CTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA\n->fliC_1,5,7_Salmonella.enterica_from-cdc-Stk1778_1,5,7__1521\n-ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC\n-TGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT\n-TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC\n-GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC\n-TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG\n-GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG\n-AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC\n-AACGACAGCTTATGCCGATAACGGTACTACATTGAATGTCTCAGGCCTTGATGATGCAGCTATCAAAGCGGCTACGGGGG\n-GTACGACTGGTGCACCTACTGTAACAGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG\n-GGCTTTACTGGTGGTGATCTCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACACTTGCGCC\n-TGGTGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAACTACACCGGTAGCTG\n-CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG\n-TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGCTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA\n-CGACGAAACGACAGGGGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACAGCGGCTAACC\n-AACTGGGTGGCGCAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT\n-GATTTCAAAGCACAGCCAGAGCTGGCGGAAGCGGCTGCTAAAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCT\n-GGCGCAGGTGGATGCACTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA\n-CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG\n-CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA\n-A\n->fliC_1,2,7_Salmonella.enterica_from-cdc-Stk2293_1,2,7__1521\n-ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC\n-TGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT\n-TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC\n-GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC\n-TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG\n-GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG\n-AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC\n-AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG\n-GTACGAATGGTGCACCTGCTGTAACAGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT\n-GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACACTTGCGCC\n-TGGTGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGCTACACCGGTAGCTG\n-CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG\n-TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGCTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA\n-CGACGAAACGACAGGGGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACAGCGGCTAACC\n-AACTGGGTGGCGCAGACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCAC\n-AACTTCAAAGCACAGCCAGAGCTGGCTGAAGTAGCTACTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT\n-GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA\n-CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG\n-CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA\n-A\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/antigens.pickle |
| b |
| Binary file SeqSero2S/seqsero2s_db/antigens.pickle has changed |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/invA_mers_dict |
| b |
| Binary file SeqSero2S/seqsero2s_db/invA_mers_dict has changed |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella.log --- a/SeqSero2S/seqsero2s_db/kmer/salmonella.log Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,24 +0,0 @@ -06/26/2023 09:03:06 AM singleSampleTool : GDUTNS--Y1.R1.raw.fastq.gz and GDUTNS--Y1.R2.raw.fastq.gz -06/26/2023 09:03:06 AM singleSampleTool : paired True -06/26/2023 09:03:06 AM singleSampleTool : fastq1 start -06/26/2023 09:03:06 AM singleFileTool :GDUTNS--Y1.R1.raw.fastq.gz -06/26/2023 09:03:06 AM singleFileTool : fastq -06/26/2023 09:03:06 AM fileExplorer :GDUTNS--Y1.R1.raw.fastq.gz -06/26/2023 09:03:54 AM singleSampleTool : fastq1 done -06/26/2023 09:03:54 AM singleSampleTool : fastq2 start -06/26/2023 09:03:54 AM singleFileTool :GDUTNS--Y1.R2.raw.fastq.gz -06/26/2023 09:03:54 AM singleFileTool : fastq -06/26/2023 09:03:54 AM fileExplorer :GDUTNS--Y1.R2.raw.fastq.gz -06/26/2023 09:04:48 AM singleSampleTool : fastq2 done -06/26/2023 09:04:48 AM singleSampleTool : weightedProfile start -06/26/2023 09:04:48 AM weightedProf -06/26/2023 09:04:48 AM singleSampleTool : weightedProfile finished -06/26/2023 09:04:48 AM singleSampleTool : getMaxCount start -06/26/2023 09:04:48 AM getMaxCount -06/26/2023 09:04:48 AM Max Support :GDUTNS--Y : {'purE': {'5': 54640}, 'dnaN': {'8': 75064}, 'thrA': {'15': 80816}, 'sucA': {'11': 61141}, 'hemD': {'11': 72516}, 'aroC': {'8': 77112}, 'hisD': {'11': 51911}} -06/26/2023 09:04:48 AM Second Max Support :GDUTNS--Y : {'purE': {'4': 48207, '456': 48207}, 'dnaN': {'1': 58680, '492': 58680}, 'thrA': {'10': 63003}, 'sucA': {'9': 58437, '46': 58437, '109': 58437, '197': 58437, '413': 58437, '570': 58437, '925': 58437, '1060': 58437}, 'hemD': {'3': 65987}, 'aroC': {'7': 67451}, 'hisD': {'1': 40164, '353': 40164}} -06/26/2023 09:04:48 AM singleSampleTool : getMaxCount end -06/26/2023 09:04:48 AM singleSampleTool : findST start -06/26/2023 09:04:48 AM findST -06/26/2023 09:04:48 AM singleSampleTool : findST end -06/26/2023 09:04:48 AM Command :['/home/shaoting/.conda/envs/seqsero2s/bin/stringMLST.py', '--predict', '-P', 'kmer/salmonella', '-1', 'GDUTNS--Y1.R1.raw.fastq.gz', '-2', 'GDUTNS--Y1.R2.raw.fastq.gz', '-o', 'GDUTNS--Y1_stringMLST.txt'] |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_35.txt --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_35.txt Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,388076 +0,0 @@\n-GTTTTTCGCCCGGGACACGCGGATTACACCTATGA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TCATAGGTGTAATCCGCGTGTCCCGGGCGAAAAAC\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TTTTTCGCCCGGGACACGCGGATTACACCTATGAG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-CTCATAGGTGTAATCCGCGTGTCCCGGGCGAAAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TTTTCGCCCGGGACACGCGGATTACACCTATGAGC\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-GCTCATAGGTGTAATCCGCGTGTCCCGGGCGAAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TTTCGCCCGGGACACGCGGATTACACCTATGAGCA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TGCTCATAGGTGTAATCCGCGTGTCCCGGGCGAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TTCGCCCGGGACACGCGGATTACACCTATGAGCAG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-CTGCTCATAGGTGTAATCCGCGTGTCCCGGGCGAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TCGCCCGGGACACGCGGATTACACCTATGAGCAGA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TCTGCTCATAGGTGTAATCCGCGTGTCCCGGGCGA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-CGCCCGGGACACGCGGATTACACCTATGAGCAGAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TTCTGCTCATAGGTGTAATCCGCGTGTCCCGGGCG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-GCCCGGGACACGCGGATTACACCTATGAGCAGAAA\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-TTTCTGCTCATAGGTGTAATCCGCGTGTCCCGGGC\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-CCCGGGACACGCGGATTACACCTATGAGCAGAAAT\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-ATTTCTGCTCATAGGTGTAATCCGCGTGTCCCGGG\taroC\t[1,305,511,512,529,530,531,532,698,1126,1173]\n-CCGGGACACGCGGATTACACCTATGAGCAGAAATA\taroC\t[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,27,28,29,30,31,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,50,51,52,53,56,59,60,61,62,63,65,67,68,69,70,72,75,76,77,78,79,80,81,82,87,88,89,90,92,93,94,98,99,100,101,102,103,105,106,107,108,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,128,129,130,131,136,137,140,141,142,143,144,147,148,150,152,153,154,155,156,158,159,160,161,162,163,164,165,168,169,170,172,175,178,179,182,183,184,185,186,187,189,193,194,195,196,197,198,199,200,201,202,203,208,209,210,213,214,215,218,221,222,225,230,231,232,233,234,244,250,254,255,256,261,262,270,277,279,282,289,290,291,294,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,315,316,319,320,321,322,324,325,326,328,329,331,332,333,336,338,341,342,343,344,345,346,347,348,349,351,353,355,357,359,360,361,362,363,364,365,367,368,369,371,373,374,375,376,379,381,382,383,386,391,397,398,400,401,403,404,407,408,409,410,411,412,413,415,416,418,419,420,421,426,428,430,431,434,435,437,438,439,440,441,442,443,444,450,451,453,454,457,462,463,464,465,468,470,472,473,474,475,476,478,480,481,482,483,484,485,488,490,492,493,494,495,496,497,498,501,504,505,507,509,511,512,514,515,519,520,523,526,527,528,529,530,531,532,533,534,535,536,537,538,540,541,542,543,544,545,546,547,548,549,551,553,558,559,560,561,564,565,566,567,568,569,571,572,575,576,579,581,582,583,584,587,589,590,592,594,595,597,599,601,602,604,608,626,627,628,630,631,634,636,640,641,646,647,650,651,652,653,658,660,662,663,664,665,666,667,668,669,670,672,673,674,675,678,679,680,681,686,688,691,692,693,698,699,700,701,702,706,711,713,717,718,719,720,723,724,725,726,727,729,732,733,734,735,736,739,740,742,747,748,749,750,751,752,753,755,756,757,759,760,761,763,764,765,766,767,770,771,773,774,776,778,779,781,782,783,784,785,786,787,788,789,790,791,792,794,795,796,799,800,801,804,805,808,809,810,811,812,814,816,818,820,821,822,823,825,826,827,830,831,832,833,834,835,836,837,838,839,840,844,845,846,850,851,854,855,856,857,858,859,860,861,862,863,864,865,866,867,871,876,884,885,886,887,891,892,893,894,896,897,898,908,909,910,911,913,914,916,917,919,922,923,924,926,927,930,931,932,935,936,937,938,940,943,944,945,947,952,953,955,956,959,960,962,965,967,968,971,974,976,978,980,982,983,988,989,990,991,992,993,994,995,999,1000,1001,1002,1003,1004,1006,1007,1009,'..b'ATCCCCTGTCTGATTAA\tthrA\t[1618]\n-TTAATCAGACAGGGGATCTGGAACTGAGCAATGGG\tthrA\t[1618]\n-CCATTGCTCAGTTCCAGATCCCCTGTCTGATTAAA\tthrA\t[1618]\n-TTTAATCAGACAGGGGATCTGGAACTGAGCAATGG\tthrA\t[1618]\n-CATTGCTCAGTTCCAGATCCCCTGTCTGATTAAAA\tthrA\t[1618]\n-TTTTAATCAGACAGGGGATCTGGAACTGAGCAATG\tthrA\t[1618]\n-ATTGCTCAGTTCCAGATCCCCTGTCTGATTAAAAA\tthrA\t[1618]\n-TTTTTAATCAGACAGGGGATCTGGAACTGAGCAAT\tthrA\t[1618]\n-TTGCTCAGTTCCAGATCCCCTGTCTGATTAAAAAT\tthrA\t[1618]\n-ATTTTTAATCAGACAGGGGATCTGGAACTGAGCAA\tthrA\t[1618]\n-TGCTCAGTTCCAGATCCCCTGTCTGATTAAAAATA\tthrA\t[1618]\n-TATTTTTAATCAGACAGGGGATCTGGAACTGAGCA\tthrA\t[1618]\n-GCCGGACGCCAGGCTGTTGAAATCGATGTCCTACT\tthrA\t[1623]\n-AGTAGGACATCGATTTCAACAGCCTGGCGTCCGGC\tthrA\t[1623]\n-CCGGACGCCAGGCTGTTGAAATCGATGTCCTACTA\tthrA\t[1623]\n-TAGTAGGACATCGATTTCAACAGCCTGGCGTCCGG\tthrA\t[1623]\n-CGGACGCCAGGCTGTTGAAATCGATGTCCTACTAG\tthrA\t[1623]\n-CTAGTAGGACATCGATTTCAACAGCCTGGCGTCCG\tthrA\t[1623]\n-GGACGCCAGGCTGTTGAAATCGATGTCCTACTAGG\tthrA\t[1623]\n-CCTAGTAGGACATCGATTTCAACAGCCTGGCGTCC\tthrA\t[1623]\n-GACGCCAGGCTGTTGAAATCGATGTCCTACTAGGA\tthrA\t[1623]\n-TCCTAGTAGGACATCGATTTCAACAGCCTGGCGTC\tthrA\t[1623]\n-ACGCCAGGCTGTTGAAATCGATGTCCTACTAGGAA\tthrA\t[1623]\n-TTCCTAGTAGGACATCGATTTCAACAGCCTGGCGT\tthrA\t[1623]\n-CGCCAGGCTGTTGAAATCGATGTCCTACTAGGAAG\tthrA\t[1623]\n-CTTCCTAGTAGGACATCGATTTCAACAGCCTGGCG\tthrA\t[1623]\n-GCCAGGCTGTTGAAATCGATGTCCTACTAGGAAGC\tthrA\t[1623]\n-GCTTCCTAGTAGGACATCGATTTCAACAGCCTGGC\tthrA\t[1623]\n-CCAGGCTGTTGAAATCGATGTCCTACTAGGAAGCG\tthrA\t[1623]\n-CGCTTCCTAGTAGGACATCGATTTCAACAGCCTGG\tthrA\t[1623]\n-CAGGCTGTTGAAATCGATGTCCTACTAGGAAGCGA\tthrA\t[1623]\n-TCGCTTCCTAGTAGGACATCGATTTCAACAGCCTG\tthrA\t[1623]\n-AGGCTGTTGAAATCGATGTCCTACTAGGAAGCGAT\tthrA\t[1623]\n-ATCGCTTCCTAGTAGGACATCGATTTCAACAGCCT\tthrA\t[1623]\n-GGCTGTTGAAATCGATGTCCTACTAGGAAGCGATG\tthrA\t[1623]\n-CATCGCTTCCTAGTAGGACATCGATTTCAACAGCC\tthrA\t[1623]\n-GCTGTTGAAATCGATGTCCTACTAGGAAGCGATGG\tthrA\t[1623]\n-CCATCGCTTCCTAGTAGGACATCGATTTCAACAGC\tthrA\t[1623]\n-CTGTTGAAATCGATGTCCTACTAGGAAGCGATGGA\tthrA\t[1623]\n-TCCATCGCTTCCTAGTAGGACATCGATTTCAACAG\tthrA\t[1623]\n-TGTTGAAATCGATGTCCTACTAGGAAGCGATGGAG\tthrA\t[1623]\n-CTCCATCGCTTCCTAGTAGGACATCGATTTCAACA\tthrA\t[1623]\n-GTTGAAATCGATGTCCTACTAGGAAGCGATGGAGC\tthrA\t[1623]\n-GCTCCATCGCTTCCTAGTAGGACATCGATTTCAAC\tthrA\t[1623]\n-TTGAAATCGATGTCCTACTAGGAAGCGATGGAGCT\tthrA\t[1623]\n-AGCTCCATCGCTTCCTAGTAGGACATCGATTTCAA\tthrA\t[1623]\n-TGAAATCGATGTCCTACTAGGAAGCGATGGAGCTC\tthrA\t[1623]\n-GAGCTCCATCGCTTCCTAGTAGGACATCGATTTCA\tthrA\t[1623]\n-GAAATCGATGTCCTACTAGGAAGCGATGGAGCTCT\tthrA\t[1623]\n-AGAGCTCCATCGCTTCCTAGTAGGACATCGATTTC\tthrA\t[1623]\n-AAATCGATGTCCTACTAGGAAGCGATGGAGCTCTC\tthrA\t[1623]\n-GAGAGCTCCATCGCTTCCTAGTAGGACATCGATTT\tthrA\t[1623]\n-AATCGATGTCCTACTAGGAAGCGATGGAGCTCTCT\tthrA\t[1623]\n-AGAGAGCTCCATCGCTTCCTAGTAGGACATCGATT\tthrA\t[1623]\n-ATCGATGTCCTACTAGGAAGCGATGGAGCTCTCTT\tthrA\t[1623]\n-AAGAGAGCTCCATCGCTTCCTAGTAGGACATCGAT\tthrA\t[1623]\n-TCGATGTCCTACTAGGAAGCGATGGAGCTCTCTTA\tthrA\t[1623]\n-TAAGAGAGCTCCATCGCTTCCTAGTAGGACATCGA\tthrA\t[1623]\n-CGATGTCCTACTAGGAAGCGATGGAGCTCTCTTAC\tthrA\t[1623]\n-GTAAGAGAGCTCCATCGCTTCCTAGTAGGACATCG\tthrA\t[1623]\n-GATGTCCTACTAGGAAGCGATGGAGCTCTCTTACT\tthrA\t[1623]\n-AGTAAGAGAGCTCCATCGCTTCCTAGTAGGACATC\tthrA\t[1623]\n-ATGTCCTACTAGGAAGCGATGGAGCTCTCTTACTT\tthrA\t[1623]\n-AAGTAAGAGAGCTCCATCGCTTCCTAGTAGGACAT\tthrA\t[1623]\n-TGTCCTACTAGGAAGCGATGGAGCTCTCTTACTTC\tthrA\t[1623]\n-GAAGTAAGAGAGCTCCATCGCTTCCTAGTAGGACA\tthrA\t[1623]\n-GTCCTACTAGGAAGCGATGGAGCTCTCTTACTTCG\tthrA\t[1623]\n-CGAAGTAAGAGAGCTCCATCGCTTCCTAGTAGGAC\tthrA\t[1623]\n-TCCTACTAGGAAGCGATGGAGCTCTCTTACTTCGG\tthrA\t[1623]\n-CCGAAGTAAGAGAGCTCCATCGCTTCCTAGTAGGA\tthrA\t[1623]\n-CCTACTAGGAAGCGATGGAGCTCTCTTACTTCGGC\tthrA\t[1623]\n-GCCGAAGTAAGAGAGCTCCATCGCTTCCTAGTAGG\tthrA\t[1623]\n-CTACTAGGAAGCGATGGAGCTCTCTTACTTCGGCG\tthrA\t[1623]\n-CGCCGAAGTAAGAGAGCTCCATCGCTTCCTAGTAG\tthrA\t[1623]\n-TACTAGGAAGCGATGGAGCTCTCTTACTTCGGCGC\tthrA\t[1623]\n-GCGCCGAAGTAAGAGAGCTCCATCGCTTCCTAGTA\tthrA\t[1623]\n-ACTAGGAAGCGATGGAGCTCTCTTACTTCGGCGCT\tthrA\t[1623]\n-AGCGCCGAAGTAAGAGAGCTCCATCGCTTCCTAGT\tthrA\t[1623]\n-CTAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTA\tthrA\t[1623]\n-TAGCGCCGAAGTAAGAGAGCTCCATCGCTTCCTAG\tthrA\t[1623]\n-TAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTAA\tthrA\t[1623]\n-TTAGCGCCGAAGTAAGAGAGCTCCATCGCTTCCTA\tthrA\t[1623]\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_aroC.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_aroC.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2512 +0,0 @@\n->aroC_1\n-GTTTTTCGCCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGCGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACTTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_2\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_3\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGTGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_4\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_5\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTTTTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_6\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGTATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_7\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_8\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAATTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGA'..b'GCAGGGGCGATCGCTAAGAAATACCTGGCGGAAAAGTTCGGTATCGAAATCCGCGGTTGTCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCAACAGGTTGAGCGTAATCCGTTCTTTTGCCCCGATGCGGATAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCTATCGGCGCGAAAGTGACGGTGATAGCGAGCGGCGTGCCGGCAGGTCTTGGCGAACCGGTATTTGATCGGCTGGATGCGGATATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAAGGTGGTGGCGCTACGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_1565\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGAAAAAGTTCGGTATCGAAATCCGTGGCTGCCTGACCAAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAACTTAATCCGTTCTTTTGCCCCGATGCGGACAAACTTGATGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCAAGCGGCGTGCCGGCAGGTCTTGGCGAACCAGTATTTGACCGACTGGACGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGTGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGTCAGAATCGCGATGAAATCACGGCACAGGGT\n->aroC_1567\n-GTCTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCACGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTAGCGGAAAAGTTCGGTATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTGTTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_1568\n-GTTTTTCGTCCGGGACACGCGGATTATACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGTGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_1569\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGTCCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGTGGCGTGCCGGCAGGGCTTGGCGAACCGGTTTTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_1571\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTAGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGCGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTTTTTGACCGACTGGATGCGGACATCGCCCATGGGCTGATGAGCATCAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGTGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n->aroC_1572\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGTGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATTGCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGGAATCACGGCGCAGGGT\n->aroC_1573\n-GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTACCGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATCGCCAAGAAATACCTGGCGGAAAAGTTCGGTATCGAAATCCGCGGCTGCCTGACCCAGATGGGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGCCCCGATGCAGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGTGACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAACCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATTAATGCGGTGAAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGCGATGAAATCACGGCGCAGGGT\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_config.txt --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_config.txt Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,10 +0,0 @@ -[loci] -aroC kmer/salmonella_aroC.tfa -dnaN kmer/salmonella_dnaN.tfa -hemD kmer/salmonella_hemD.tfa -hisD kmer/salmonella_hisD.tfa -purE kmer/salmonella_purE.tfa -sucA kmer/salmonella_sucA.tfa -thrA kmer/salmonella_thrA.tfa -[profile] -profile kmer/salmonella_profile.txt |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_dnaN.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_dnaN.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2440 +0,0 @@\n->dnaN_1\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAGGCGTCTTTACCTAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGTGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_2\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGTGAAAACCCGCTGCGCGTGCAG\n->dnaN_3\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGTTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_4\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_5\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCCACGCTTCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_6\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGTACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_7\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAATCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_8\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGTGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACACTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGCAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGTCTGGCGGT'..b'GAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_1326\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCTACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGCAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCATTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGTGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_1328\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAACGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGTGAAAACCCGCTGCGCGTGCAG\n->dnaN_1329\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACACTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAAGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_1330\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGCGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCTTAATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGTTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_1331\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGTGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCTCATCAGGACGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_1333\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCGGGTGCTACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGTCGTTCAGTTGGAAGGCGATCGGATGTTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n->dnaN_1334\n-ATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCATGAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCGGAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGTTGGTGCGTTCTGGCCGTAGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAAAGCGAAGTTGAATTTACGCTGCCACAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAGTTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAAGGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCGCTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTGATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAG\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_hemD.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_hemD.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2326 +0,0 @@\n->hemD_1\n-GCAACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACTCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGACGAAACTGGCCTGCGTCGCCGCGCTATTTCTCGATTGGCCGCACTACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGTTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_2\n-GCAACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACTCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGACGAAACTGGCCTGCGTCGCCGCGCTATTTCTCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGTTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_3\n-GCGACACTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_4\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGCCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_5\n-GCGACACTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTAATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_6\n-GCGACGCTCGCGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAAATGTTGCAA\n->hemD_7\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTAATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_8\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_9\n-GCGACGCTGACGAAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGACACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATG'..b'GACGTTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCCCACGCCCAACTCCAGCGAGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGTCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGTCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGTCGCGAACTGCTGGGCGAAACCCTGACAGCTCACGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGAAGTGCGAAACATTACGATGGCGCAGAAGAGGCGATGCGCTGGCATACTCGCGGCGTAACGACGCTTGTTGTCACCAGCGGCGAGATGTTGCAA\n->hemD_1265\n-GCGACTCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCTCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACACTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_1268\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTGGCGCCGCGCTATTTTGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_1269\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTGGCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGTGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_1270\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCCCACGCCCAGATCCAGCAGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGATTCGATATTCGTTATCCATTGGGTCGGGAAATCAGCGAAGTCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGTCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAATTTTTGTGAATGTTATCAACGAAGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATGCTCGCGGCATAACAACGCTTGTTGTCACCAGCGGCGAGATGTTGCAA\n->hemD_1271\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGCCGAAACTGGCCTGTGGCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCGCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_1272\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTGGCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACACTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_1273\n-GCGAAGCTGACGGAAAAAGATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCAAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAA\n->hemD_1275\n-GCGACGCTGACGGAAAACGATCTGGTTTTTGCCCTTTCACAGCACGCTGTCGCCTTTGCTCACACCCAGCTCCAGCGGGATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAAGCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGTGGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGTTTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGCTGGCATACTCGCGGCGTAACAACGCTTGTTGTCACCAGCGGCGAGATGTTGCAA\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_hisD.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_hisD.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,3420 +0,0 @@\n->hisD_1\n-ATTGCGGGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCACCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGGCACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_2\n-ATTGCAGGATGCCAGATCGTGGTTCTGTGCTCGCCACCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_3\n-ATTGCGGGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCACCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAATACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGGCACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_4\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCCCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAGCTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTAATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_5\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCAGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTACTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_6\n-ATTGCGGGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCAGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGATGATCCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_7\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAACGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCTGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCAGAACTGCCGCGCGCGGACACCGCCAGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_8\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCG'..b'GCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAATCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTCGTGACCGAAGCCAAACGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACGCCGGATTTCGTCGCTTCTGACCTGCTTTCCCAGGCAGAACACGGCCCGGATTCACAGGTGATTCTTCTGACGCCGGATGCCGACATCGCCCGCAAGGTAGCGGAGGCGGTAGAACGTCAACTGGCTGAACTGCCGCGCGCGGAAACCGCCCGTCAGGCTTTGCGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1898\n-ATTGCGGGATGCCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCACAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTTGCAGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1899\n-ATTGCGGGATGTCAGAAAGTGGTTCTGTGCTCGCCGCCGCCCATCGCCGATGAAATCCTCTATGCGGCACAACTGTGTGGCATACAGGAGATCTTTAACGTCGGCGGCTCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAATCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAATGCTTTTGTAACTGAAGCCAAGCGTCAGGTCAGTCAGCGTCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACGCCGGACTTCGTCGCTTCTGACCTGCTCTCCCAGGCAGAACACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTAACATCGCCCGCAGGGTGGCGGAGGCGGTAGAACGTCAACTGGCTGAACTGCCGCGCGCGGACACCGCCCGTCAGGCTTTGCGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1900\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAACGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCGCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCTGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCAGAACTGCCGCGTGCGGACACCGCCAGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1902\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAGGCAGAACACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCTGATGCTCACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1903\n-ATTGCGGGATGCCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCACGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCTTCTGACCTGCTCTCCCAGGCTGAGCACGGTCCGGATTCCCAGGTGATTCTGCTGACGCCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1904\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCGCAACTGTGTGGCGTGCGGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCCTTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAACGCCTCGACGGCGCGGCTATCGATATGCCTGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTCGCGTCTGACCTGCTCTCCCAAGCTGAGCACGGTCCGGATTCGCAGGTGATCCTGCTGACGCCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAGCTGCCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n->hisD_1905\n-ATTGCGGGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCGGCACAGCTATGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCACAGGCGATTGCCGCTCTGGCCTTCGGCAGCGAATCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAATGCTTTTGTAACTGAAGCCAAGCGTCAGGTCAGTCAGCGTCTCGACGGCGTGGCTATCGATATGCCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACGCCGGACTTCGTCGCTTCTGACCTGCTCTCCCAGGCAGAACACGGCCCGGATTCCCAGGTGATCCTGCTGACGCCGGATGCTGACATCGCCCGCAGGGTGGCGGAGGCGGTAGAACGTCAACTGGCTGAACTGCCGCGCGCGGACACCGCCCGTCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGATTTAGCGCAGTGCGTC\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_profile.txt --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_profile.txt Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,9123 +0,0 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|
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_purE.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_purE.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2708 +0,0 @@\n->purE_1\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCACACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGGGCGGCGAACGCCGCACTGCTGGCAGCGCAAATTTTGGCTACGCATGATAGCGCGCTGCATCGGCGCATCGCCGAC\n->purE_2\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n->purE_3\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACACTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCACAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCCGAC\n->purE_4\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n->purE_5\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_6\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_7\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTTTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_8\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_9\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTTTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACACTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n->purE_10\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCACATCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTACCGGTACAAAGCGCTGCGCTAAGCGGTGTGGATAGCCTCTACTCCATCGTGCAGATG'..b'TCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_1560\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_1562\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTGCCGGTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGGGCGGCGAACGCCGCACTGCTGGCAGCGCAAATTTTGGCTACGCATGATAGCGCGCTGCATCGGCGCATCGCCGAC\n->purE_1563\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCAGTGGGTACGCTGGCGATCGGCAAAGCCGGTGCCGCGAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCCGAC\n->purE_1564\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_1565\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_1566\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_1568\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTCTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTTTACTCCATTGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n->purE_1569\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAGCTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGCGCGGCACACCTGCCGGGAATGATTGCGGCAAAAACTCTGGTCCCGGTACTCGGCGTACCGGTACAAAGCGCTGCGCTAAGCGGTGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCACTGCTGGCAGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATTGCCGAC\n->purE_1570\n-AGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATTCTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGGGCGGGCGGCGCGGCACACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCGGTACAAAGCGCTGCGCTAAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGAC\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_sucA.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_sucA.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2532 +0,0 @@\n->sucA_1\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCTATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGTCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAACATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACTGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACCGACTGGACGAACCGAGCAGTAATAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_2\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_3\n-AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATTACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_4\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACTGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCCCGTCTGGACCGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATTACCATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_5\n-AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGAACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAACATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCCCGTCTGGACCGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_6\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_7\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_8\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCCGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGTGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACTGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGT'..b'CCGATGCTGAAAGAGATGGTTCGCCATGCGGGTAATAGCGGCACTCGCGAAGTGGTGCTGGGTATGGCGCACCGCGGTCGCCTGAACGTACTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAGCATAAAGAACATCTTGGCACCGGCGATGTGAAGTACCACATGGGCTTCTCGTCAGATATCGAAACGGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATCGTGAGCCCGGTGGTGATGGGATCTGTGCGTGCGCGTTTGGATAGACTGGACGAACCGAGCAGCAACAAAGTGCTACCCATCACCATTCATGGCGATGCGGCAGTCACCGGCCAGGGCGTGGTTCAG\n->sucA_1409\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCAGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_1410\n-AAACGCTTTCTGAACGAACTAACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCCGGTGCGAAACGTTTCTCGCTGGAGGGGGGAGATGCTCTGGTACCCATGTTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGGTCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTTGCCGGTAAGCATAAAGAACATCTTGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGCCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCACCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCTCGTCTGGACAGACTGGACGAGCCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_1411\n-AAACGTTTCCTAAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_1412\n-AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCACTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_1415\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGTGCCCGTCTGGACCGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_1416\n-AAACGTTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTTGAGGGGGGAGATGCGTTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATTTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n->sucA_1417\n-AAACGCTTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGTGCCAAATTCCCGGGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATGGTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGTGGTCGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTTGCCGGTAAGCATAAAGAACATCTGGGTACTGGCGACGTGAAGTATCACATGGGCTTCTCGTCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCATCTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACCGACTGGACGAACCGAGCAGTAATAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGCCAGGGCGTGGTTCAG\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_thrA.tfa --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_thrA.tfa Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2946 +0,0 @@\n->thrA_1\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGACTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_2\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAACCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_3\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCATCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_4\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCACGTCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCATCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_5\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_6\n-GTGCTGGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGACTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTGAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCTGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_7\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTTCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTCAAAGGGATCTCTAACCTTAACAATATGGCGATGTTTAGCGTCTCCGGCCCTGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_8\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGAT'..b'CCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1615\n-GTGCTTGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCAGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCAGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1616\n-GTACTGGGCCGTAACGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCGTGTTTACGTGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATGATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGTCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTACTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1617\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTTCTTCACCCTCGTACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAACCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1618\n-GTGCTGGGCCGTAATGGTTCCGACTATTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATTGCTCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTACTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1621\n-GTGCTGGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGTGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGTGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCTGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1623\n-GTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACTAGGAAGCGATGGAGCTCTCTTACTTCGGCGCTAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n->thrA_1624\n-GTGCTGGGGCGTAATGGCTCTGACTACTCTGCCGCCGTGCTGGCCGCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGTGTGTATACCTGTGACCCGCGCCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATGGAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATTACGCCCATCGCCCAGTTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATCGGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATGGCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTTTTCGCCGCCATGTCTCGCGCCGGAATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAGTACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC\n' |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/kmer/salmonella_weight.txt --- a/SeqSero2S/seqsero2s_db/kmer/salmonella_weight.txt Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -purE_631 0.7904408017272534 -purE_748 0.83309951166174 -purE_749 0.7904408017272534 -purE_781 0.8757582215962267 -purE_866 0.7904408017272534 -purE_868 0.8180434963907447 -purE_971 1.076505091876164 -purE_1502 0.83309951166174 -purE_1537 1.0539210689696712 |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/mlst.pickle |
| b |
| Binary file SeqSero2S/seqsero2s_db/mlst.pickle has changed |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/seqsero2s_db/special.pickle |
| b |
| Binary file SeqSero2S/seqsero2s_db/special.pickle has changed |
| b |
| diff -r 4dbbf92ff30a -r 6041d8f4eeeb SeqSero2S/setup.py --- a/SeqSero2S/setup.py Fri May 15 17:55:16 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,31 +0,0 @@ -import os, sys -from distutils.core import setup -from setuptools import find_packages - -def readme(): - with open('README.md') as f: - return f.read() - -setup(name='SeqSero2S', - #version=open("version.py").readlines()[-1].split()[-1].strip("\"'"), - version='1.1.4', - description='Salmonella serotyping', - long_description=readme(), - classifiers=[ - 'Development Status :: 3 - Alpha', - 'License :: OSI Approved :: GNU General Public License v2 (GPLv2)', - 'Programming Language :: Python :: 3', - 'Topic :: Text Processing :: Linguistic', - ], - keywords='Salmonella serotyping bioinformatics WGS', - url='https://github.com/denglab/SeqSero2S/', - author='Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng', - author_email='zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu', - license='GPLv2', - scripts=["bin/deinterleave_fastq.sh","bin/Initial_Conditions_SS2S.py","bin/Initial_Conditions_SS2.py","bin/SeqSero2S.py","bin/SeqSero2_update_kmer_database.py"], - packages=[""], - include_package_data = True, - install_requires=['biopython~=1.73'], - data_files=[("seqsero2s_db",["seqsero2s_db/mlst.pickle","seqsero2s_db/antigens.pickle","seqsero2s_db/H_and_O_and_specific_genes.fasta","seqsero2s_db/invA_mers_dict","seqsero2s_db/special.pickle"]),("seqsero2s_db/kmer",["seqsero2s_db/kmer/salmonella_35.txt","seqsero2s_db/kmer/salmonella_config.txt","seqsero2s_db/kmer/salmonella_hemD.tfa","seqsero2s_db/kmer/salmonella.log","seqsero2s_db/kmer/salmonella_purE.tfa","seqsero2s_db/kmer/salmonella_thrA.tfa","seqsero2s_db/kmer/salmonella_aroC.tfa","seqsero2s_db/kmer/salmonella_dnaN.tfa","seqsero2s_db/kmer/salmonella_hisD.tfa","seqsero2s_db/kmer/salmonella_profile.txt","seqsero2s_db/kmer/salmonella_sucA.tfa","seqsero2s_db/kmer/salmonella_weight.txt"])], - zip_safe=False, -) |
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| diff -r 4dbbf92ff30a -r 6041d8f4eeeb seqsero2S.xml --- a/seqsero2S.xml Fri May 15 17:55:16 2026 +0000 +++ b/seqsero2S.xml Fri May 15 19:51:16 2026 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="seqsero2s" name="SeqSero2S" version="1.1.4+galaxytrakr+1"> +<tool id="seqsero2s" name="SeqSero2S" version="1.1.4+galaxytrakr"> <description>Simplified Salmonella serotype prediction</description> <requirements> <container type="docker">quay.io/galaxytrakr/seqsero2s:1.1.3</container> |