--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.0/bin/process_centrifuge_output.py	Thu Aug 04 10:45:55 2022 -0400
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+
+import os
+import argparse
+import logging as log
+import pandas as pd
+import numpy as np
+from Bio import SeqIO
+
+
+def main():
+    # READ IN ARGUMENTS
+    desc = """
+    This script is part of the centriflaken pipeline: It processes centrifuge
+    output and produces either a filtered FASTQ or a text file of FASTQ IDs based
+    on the supplied taxa/bug
+    """
+    parser = argparse.ArgumentParser(prog='process_centrifuge_output.py', description=desc)
+    parser.add_argument("-v", dest='verbose', action="store_true", help="For more verbose output")
+    parser.add_argument("-i", dest='input_fastq', required=False,
+        help="Path to input FASTQ file (same as input to centrifuge). If not mentioned, \
+            a text file of sequence IDs are produced instead of a FASTQ file")
+    parser.add_argument("-t", dest='taxa_filtered_fastq_file', required=True,
+        help="Path to output FASTQ or output text file filtered by the taxa specified")
+    parser.add_argument("-r", dest='cent_report', required=True, help="Path to centrifuge report")
+    parser.add_argument("-o", dest='cent_output', required=True, help="Path to centrifuge output")
+    parser.add_argument("-b", dest='bug', required=True,
+        help="Name or fragment of name of the bug by which reads are extracted")
+    args = parser.parse_args()
+
+    # MORE INFO IF VERBOSE
+    if args.verbose:
+        log.basicConfig(format="%(levelname)s: %(message)s", level=log.DEBUG)
+    else:
+        log.basicConfig(format="%(levelname)s: %(message)s")
+
+    # ASSIGN VARIABLES
+    input_fastq = args.input_fastq
+    taxa_filtered_fastq_file = args.taxa_filtered_fastq_file
+    cent_report = args.cent_report
+    cent_output = args.cent_output
+    bug = args.bug
+    report_col_list = ["name", "taxID"]
+    output_col_list = ["taxID", "readID"]
+
+    # Match and filter taxa names and ids from centrifuge report file
+    report_df = pd.read_csv(cent_report, delimiter="\t", usecols=report_col_list)
+    report_df['name'] = report_df['name'].str.lower()
+    filt_report_df = report_df[report_df['name'].str.contains(bug.lower())]
+    #print("\nMatching taxa names and ids:\n",filt_report_df)
+    taxID_list = filt_report_df['taxID']
+
+    # Match the above tax ids to read ids from centrifuge output file and deduplicate
+    output_df = pd.read_csv(cent_output, delimiter="\t", usecols=output_col_list)
+    filt_output_df = output_df.loc[output_df['taxID'].isin(taxID_list)]
+    readID_list = filt_output_df['readID']
+    readID_dedup_list = np.unique(readID_list)
+    TF=open(taxa_filtered_fastq_file, "w")
+
+    if (not input_fastq):
+        # print("\nFILTERED READ ID LIST:\n", readID_dedup_list)
+        for ID in readID_dedup_list:
+            TF.write(f"{ID}\n")
+    else:
+        # Extract filtered reads from input fastq and write to output fastq
+        print ("Indexing reads..")
+        rec = SeqIO.index(input_fastq,"fastq")
+        for i in readID_dedup_list:
+            if i in rec:
+                SeqIO.write(rec[i], TF, "fastq")
+
+    TF.close()
+
+if __name__ == "__main__":
+    main()
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