annotate tools/fastq/fastq_filter_by_id.py @ 0:10e963c79a45

Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository

#!/usr/bin/env python
"""Filter a FASTQ file with IDs from a tabular file, e.g. from BLAST.

Takes five command line options, tabular filename, ID column numbers
(comma separated list using one based counting), input FASTA filename, and
two output FASTA filenames (for records with and without the given IDs).

If either output filename is just a minus sign, that file is not created.
This is intended to allow output for just the matched (or just the non-matched)
records.

Note in the default NCBI BLAST+ tabular output, the query sequence ID is
in column one, and the ID of the match from the database is in column two.
Here sensible values for the column numbers would therefore be "1" or "2".

This script is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved.
See accompanying text file for licence details (MIT/BSD style).

This is version 0.0.2 of the script.
"""
import sys
from galaxy_utils.sequence.fastq import fastqReader, fastqWriter

def stop_err( msg ):
    sys.stderr.write( msg )
    sys.exit()

#Parse Command Line
try:
    tabular_file, cols_arg, in_file, out_positive_file, out_negative_file = sys.argv[1:]
except ValueError:
    stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
try:
    columns = [int(arg)-1 for arg in cols_arg.split(",")]
except ValueError:
    stop_err("Expected list of columns (comma separated integers), got %s" % cols_arg)

#Read tabular file and record all specified identifiers
ids = set()
handle = open(tabular_file, "rU")
if len(columns)>1:
    #General case of many columns
    for line in handle:
        if line.startswith("#"):
            #Ignore comments
            continue
        parts = line.rstrip("\n").split("\t")
        for col in columns:
            ids.add(parts[col])
    print "Using %i IDs from %i columns of tabular file" % (len(ids), len(columns))
else:
    #Single column, special case speed up
    col = columns[0]
    for line in handle:
        if not line.startswith("#"):
            ids.add(line.rstrip("\n").split("\t")[col])
    print "Using %i IDs from tabular file" % (len(ids))
handle.close()

#Write filtered FASTQ file based on IDs from tabular file
reader = fastqReader(open(in_file, "rU"))
if out_positive_file != "-" and out_negative_file != "-":
    print "Generating two FASTQ files"
    positive_writer = fastqWriter(open(out_positive_file, "w"))
    negative_writer = fastqWriter(open(out_negative_file, "w"))
    for record in reader:
        #The [1:] is because the fastaReader leaves the @ on the identifer.
        if record.identifier and record.identifier.split()[0][1:] in ids:
            positive_writer.write(record)
        else:
            negative_writer.write(record)
    positive_writer.close()
    negative_writer.close()
elif out_positive_file != "-":
    print "Generating matching FASTQ file"
    positive_writer = fastqWriter(open(out_positive_file, "w"))
    for record in reader:
        #The [1:] is because the fastaReader leaves the @ on the identifer.
        if record.identifier and record.identifier.split()[0][1:] in ids:
            positive_writer.write(record)
    positive_writer.close()
elif out_negative_file != "-":
    print "Generating non-matching FASTQ file"
    negative_writer = fastqWriter(open(out_negative_file, "w"))
    for record in reader:
        #The [1:] is because the fastaReader leaves the @ on the identifer.
        if not record.identifier or record.identifier.split()[0][1:] not in ids:
            negative_writer.write(record)
    positive_writer.close()
    negative_writer.close()
else:
    stop_err("Neither output file requested")
reader.close()