Mercurial > repos > jasmine_amir > snrqk
changeset 0:5960f43113c6
"planemo upload commit 4031103614dfaf8b7c840f3867166e448c1fd6c7"
| author | jasmine_amir |
|---|---|
| date | Fri, 22 Apr 2022 22:27:01 -0400 |
| parents | |
| children | b3e3fa1f38c1 |
| files | README.md SNRQK.py snrqk.xml test-data/joinSamBow.txt test-data/joinSamBow_both.txt test-data/joinSamBow_nc.txt test-data/joinSamBow_pc.txt test-data/snrqk_result.tsv test-data/snrqk_resultFloat.tsv test-data/snrqk_resultjoinSamBow.txt.tsv test-data/snrqk_resultjoinSamBow_both.txt.tsv test-data/snrqk_resultjoinSamBow_nc.txt.tsv test-data/snrqk_resultjoinSamBow_pc.txt.tsv |
| diffstat | 13 files changed, 249 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,1 @@ +# snrqk \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNRQK.py Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 +# coding: utf-8 +########################################################### +########################################################### +## Jasmine Amirzadegan +## 2022 APRIL 14 +########################################################### +## SNRQC.py: +## compute QC metrics specific to SSQuAWK v4 + workflows +## usage: python SNRQC.py intermediateSSQuAWKfile.txt +## python 3.7 +########################################################### +import pandas as pd +import sys + +fn = sys.argv[1] +df = pd.read_csv(fn, sep = "\t", header = 0) + + + +if (df['Sample'].str.contains('negativeControl')).any(): + m = df.loc[ (df['Sample'].str.contains('negativeControl')) ] + noise = m['readsAlignPassFilt'] + SNR = [] + + for i in df['readsAlignPassFilt']: + SNR.append(i/noise.item()) + #[float(j) for j in SNR] + df['SNR'] = SNR + +else: + df['SNR'] = "NA" + +#print(df) +#fn1 = fn.split("/")[1] +#df.to_csv('test-data/snrqk_result' + fn1 + '.tsv', sep="\t") +df.to_csv('snrqk_result.tsv', sep='\t')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snrqk.xml Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,31 @@ +<tool id="snrqk" name="SNRQK" version="1" profile="20.09"> + <description>Compute SSQuAWK QC metrics within SSQuAWK version 4+ workflow</description> + <requirements> + <requirement type="package" version="3.7.12">python</requirement> + <requirement type="package" version="0.14.1">pandas</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/SNRQK.py $input +]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Source file"/> + </inputs> + <outputs> + <data format="tabular" label="snrqk_result" name = "results" from_work_dir="snrqk_result.tsv" /> + </outputs> + <tests> + <test> + <param name="input" value = "joinSamBow_nc.txt" ftype = "tabular"/> + <output name="results" file="snrqk_result.tsv" /> + </test> + </tests> + <help> "This tool computes QC metrics within the SSQuAWK version 4+ workflow." + </help> + <citations> + <citation type="bibtex"> + @misc{SSQuAWK, + title={SSQuAWK}, url={https://www.protocols.io/view/wastewater-qc-workflow-in-galaxytrakr-ssquawk3-kxygxzk5dv8j/v5}}, + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joinSamBow.txt Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ +Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt +SRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 +SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 +SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 +SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 +SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 +SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 +SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 +SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 +SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 +SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 +SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 +SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 +SRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 +SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 +SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 +SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 +SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joinSamBow_both.txt Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ +Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt +positiveControlSRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 +SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 +SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 +SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 +SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 +SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 +SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 +SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 +SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 +SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 +SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 +SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 +negativeControlSRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 +SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 +SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 +SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 +SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joinSamBow_nc.txt Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ +Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt +SRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 +SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 +SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 +SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 +SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 +SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 +SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 +SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 +SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 +SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 +SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 +SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 +negativeControlSRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 +SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 +SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 +SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 +SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joinSamBow_pc.txt Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ +Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt +positiveControlSRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 +SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 +SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 +SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 +SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 +SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 +SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 +SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 +SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 +SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 +SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 +SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 +SRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 +SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 +SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 +SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 +SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snrqk_result.tsv Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ + Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt SNR +0 SRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 18 +1 SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 24 +2 SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 7 +3 SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 2 +4 SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 3 +5 SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 2 +6 SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 3 +7 SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 2 +8 SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 5 +9 SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 8 +10 SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 2 +11 SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 3 +12 negativeControlSRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 1 +13 SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 12 +14 SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 3 +15 SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 4 +16 SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151 3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snrqk_resultFloat.tsv Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ + Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt SNR +0 SRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 18.59342607746863 +1 SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 24.051827605019096 +2 SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 7.359247135842881 +3 SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 2.878887070376432 +4 SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 3.359519912711402 +5 SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 2.8396072013093288 +6 SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 3.0 +7 SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 2.544189852700491 +8 SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 5.323649754500818 +9 SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 8.675941080196399 +10 SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 2.9743589743589745 +11 SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 3.4725859247135844 +12 negativeControlSRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 1.0 +13 SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 12.237315875613747 +14 SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 3.8709765411893073 +15 SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 4.33456082924168 +16 SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151 3.1479814511729405
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snrqk_resultjoinSamBow.txt.tsv Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ + Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt SNR +0 SRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 NA +1 SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 NA +2 SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 NA +3 SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 NA +4 SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 NA +5 SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 NA +6 SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 NA +7 SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 NA +8 SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 NA +9 SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 NA +10 SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 NA +11 SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 NA +12 SRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 NA +13 SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 NA +14 SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 NA +15 SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 NA +16 SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151 NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snrqk_resultjoinSamBow_both.txt.tsv Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ + Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt SNR +0 positiveControlSRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 18.59342607746863 +1 SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 24.051827605019096 +2 SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 7.359247135842881 +3 SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 2.878887070376432 +4 SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 3.359519912711402 +5 SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 2.8396072013093288 +6 SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 3.0 +7 SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 2.544189852700491 +8 SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 5.323649754500818 +9 SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 8.675941080196399 +10 SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 2.9743589743589745 +11 SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 3.4725859247135844 +12 negativeControlSRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 1.0 +13 SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 12.237315875613747 +14 SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 3.8709765411893073 +15 SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 4.33456082924168 +16 SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151 3.1479814511729405
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snrqk_resultjoinSamBow_nc.txt.tsv Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ + Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt SNR +0 SRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 18.59342607746863 +1 SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 24.051827605019096 +2 SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 7.359247135842881 +3 SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 2.878887070376432 +4 SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 3.359519912711402 +5 SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 2.8396072013093288 +6 SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 3.0 +7 SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 2.544189852700491 +8 SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 5.323649754500818 +9 SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 8.675941080196399 +10 SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 2.9743589743589745 +11 SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 3.4725859247135844 +12 negativeControlSRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 1.0 +13 SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 12.237315875613747 +14 SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 3.8709765411893073 +15 SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 4.33456082924168 +16 SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151 3.1479814511729405
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snrqk_resultjoinSamBow_pc.txt.tsv Fri Apr 22 22:27:01 2022 -0400 @@ -0,0 +1,18 @@ + Sample nReads readsAlignPassFilt avgQual readsAligned avgQualPassFilt avgLen avgLenPassFilt SNR +0 positiveControlSRR16828363.fastq.gz 632664 136327 37.8 138637 37.9 151 151 NA +1 SRR16828364.fastq.gz 458116 176348 37.8 179913 37.9 151 151 NA +2 SRR16828365.fastq.gz 351980 53958 37.8 54928 37.9 151 151 NA +3 SRR16828366.fastq.gz 322968 21108 37.8 21470 37.9 151 151 NA +4 SRR16828367.fastq.gz 250920 24632 37.8 25076 37.9 151 151 NA +5 SRR16828368.fastq.gz 261146 20820 37.8 21269 37.9 151 151 NA +6 SRR16828369.fastq.gz 333366 21996 37.7 22519 37.9 151 151 NA +7 SRR16828370.fastq.gz 384632 18654 37.7 19129 37.9 151 151 NA +8 SRR16828371.fastq.gz 403370 39033 37.8 39675 37.9 151 151 NA +9 SRR16828372.fastq.gz 325846 63612 37.8 64765 37.9 151 151 NA +10 SRR16828373.fastq.gz 271852 21808 37.8 22257 37.9 151 151 NA +11 SRR16828374.fastq.gz 307272 25461 37.8 25870 37.9 151 151 NA +12 SRR16828375.fastq.gz 148574 7332 37.8 7462 38.0 151 151 NA +13 SRR16828376.fastq.gz 479676 89724 37.8 91360 37.9 151 151 NA +14 SRR16828377.fastq.gz 401236 28382 37.8 28936 37.9 151 151 NA +15 SRR16828378.fastq.gz 236128 31781 37.7 32559 37.9 151 151 NA +16 SRR16828379.fastq.gz 288528 23081 37.8 23564 37.9 151 151 NA