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1 #!/usr/bin/env python
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2
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3 import os
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4 import argparse
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5 import logging as log
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6 import pandas as pd
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7 import numpy as np
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8 from Bio import SeqIO
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9
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10
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11 def main():
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12 # READ IN ARGUMENTS
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13 desc = """
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14 This script is part of the centriflaken pipeline: It processes centrifuge
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15 output and produces either a filtered FASTQ or a text file of FASTQ IDs based
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16 on the supplied taxa/bug
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17 """
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18 parser = argparse.ArgumentParser(prog='process_centrifuge_output.py', description=desc)
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19 parser.add_argument("-v", dest='verbose', action="store_true", help="For more verbose output")
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20 parser.add_argument("-i", dest='input_fastq', required=False,
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21 help="Path to input FASTQ file (same as input to centrifuge). If not mentioned, \
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22 a text file of sequence IDs are produced instead of a FASTQ file")
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23 parser.add_argument("-t", dest='taxa_filtered_fastq_file', required=True,
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24 help="Path to output FASTQ or output text file filtered by the taxa specified")
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25 parser.add_argument("-r", dest='cent_report', required=True, help="Path to centrifuge report")
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26 parser.add_argument("-o", dest='cent_output', required=True, help="Path to centrifuge output")
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27 parser.add_argument("-b", dest='bug', required=True,
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28 help="Name or fragment of name of the bug by which reads are extracted")
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29 args = parser.parse_args()
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30
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31 # MORE INFO IF VERBOSE
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32 if args.verbose:
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33 log.basicConfig(format="%(levelname)s: %(message)s", level=log.DEBUG)
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34 else:
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35 log.basicConfig(format="%(levelname)s: %(message)s")
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36
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37 # ASSIGN VARIABLES
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38 input_fastq = args.input_fastq
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39 taxa_filtered_fastq_file = args.taxa_filtered_fastq_file
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40 cent_report = args.cent_report
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41 cent_output = args.cent_output
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42 bug = args.bug
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43 report_col_list = ["name", "taxID"]
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44 output_col_list = ["taxID", "readID"]
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45
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46 # Match and filter taxa names and ids from centrifuge report file
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47 report_df = pd.read_csv(cent_report, delimiter="\t", usecols=report_col_list)
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48 report_df['name'] = report_df['name'].str.lower()
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49 filt_report_df = report_df[report_df['name'].str.contains(bug.lower())]
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50 #print("\nMatching taxa names and ids:\n",filt_report_df)
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51 taxID_list = filt_report_df['taxID']
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52
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53 # Match the above tax ids to read ids from centrifuge output file and deduplicate
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54 output_df = pd.read_csv(cent_output, delimiter="\t", usecols=output_col_list)
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55 filt_output_df = output_df.loc[output_df['taxID'].isin(taxID_list)]
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56 readID_list = filt_output_df['readID']
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57 readID_dedup_list = np.unique(readID_list)
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58 TF=open(taxa_filtered_fastq_file, "w")
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59
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60 if (not input_fastq):
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61 # print("\nFILTERED READ ID LIST:\n", readID_dedup_list)
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62 for ID in readID_dedup_list:
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63 TF.write(f"{ID}\n")
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64 else:
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65 # Extract filtered reads from input fastq and write to output fastq
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66 print ("Indexing reads..")
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67 rec = SeqIO.index(input_fastq,"fastq")
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68 for i in readID_dedup_list:
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69 if i in rec:
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70 SeqIO.write(rec[i], TF, "fastq")
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71
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72 TF.close()
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73
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74 if __name__ == "__main__":
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75 main() |
