annotate tools/filters/seq_filter_by_id.py @ 0:5844f6a450ed

Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository

#!/usr/bin/env python
"""Filter a FASTA, FASTQ or SSF file with IDs from a tabular file.

Takes six command line options, tabular filename, ID column numbers (comma
separated list using one based counting), input filename, input type (e.g.
FASTA or SFF) and two output filenames (for records with and without the
given IDs, same format as input sequence file).

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.

When filtering an SFF file, any Roche XML manifest in the input file is
preserved in both output files.

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 tool is a short Python script which requires Biopython 1.54 or later
for SFF file support. If you use this tool in scientific work leading to a
publication, please cite the Biopython application note:

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

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 0.0.1 of the script.
"""
import sys

def stop_err(msg, err=1):
    sys.stderr.write(msg.rstrip() + "\n")
    sys.exit(err)

#Parse Command Line
try:
    tabular_file, cols_arg, in_file, seq_format, out_positive_file, out_negative_file = sys.argv[1:]
except ValueError:
    stop_err("Expected six 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)

if out_positive_file == "-" and out_negative_file == "-":
    stop_err("Neither output file requested")


#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()


if seq_format.lower()=="sff":
    #Now write filtered SFF file based on IDs from BLAST file
    try:
        from Bio.SeqIO.SffIO import SffIterator, SffWriter
    except ImportError:
        stop_err("Requires Biopython 1.54 or later")

    try:
        from Bio.SeqIO.SffIO import ReadRocheXmlManifest
    except ImportError:
        #Prior to Biopython 1.56 this was a private function
        from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
    in_handle = open(in_file, "rb") #must be binary mode!
    try:
        manifest = ReadRocheXmlManifest(in_handle)
    except ValueError:
        manifest = None
    #This makes two passes though the SFF file with isn't so efficient,
    #but this makes the code simple.
    if out_positive_file != "-":
        out_handle = open(out_positive_file, "wb")
        writer = SffWriter(out_handle, xml=manifest)
        in_handle.seek(0) #start again after getting manifest
        pos_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id in ids)
        out_handle.close()
    if out_negative_file != "-":
        out_handle = open(out_negative_file, "wb")
        writer = SffWriter(out_handle, xml=manifest)
        in_handle.seek(0) #start again
        neg_count = writer.write_file(rec for rec in SffIterator(in_handle) if rec.id not in ids)
        out_handle.close()
    #And we're done
    in_handle.close()
    #At the time of writing, Galaxy doesn't show SFF file read counts,
    #so it is useful to put them in stdout and thus shown in job info.
    if out_positive_file != "-" and out_negative_file != "-":
        print "%i with and %i without specified IDs" % (pos_count, neg_count)
    elif out_positive_file != "-":
        print "%i with specified IDs" % pos_count
    elif out_negative_file != "-":
        print "%i without specified IDs" % neg_count
elif seq_format.lower()=="fasta":
    #Write filtered FASTA file based on IDs from tabular file
    from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
    reader = fastaReader(open(in_file, "rU"))
    if out_positive_file != "-" and out_negative_file != "-":
        print "Generating two FASTA files"
        positive_writer = fastaWriter(open(out_positive_file, "w"))
        negative_writer = fastaWriter(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 FASTA file"
        positive_writer = fastaWriter(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 FASTA file"
        negative_writer = fastaWriter(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)
        negative_writer.close()
elif seq_format.lower().startswith("fastq"):
    #Write filtered FASTQ file based on IDs from tabular file
    from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
    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)
        negative_writer.close()
else:
    stop_err("Unsupported file type %r" % seq_format)