Mercurial > repos > peterjc > fasta_filter_by_id
view tools/fasta_filter_by_id/fasta_filter_by_id.py @ 3:812383b5d3b8 draft default tip
v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
author | peterjc |
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date | Fri, 03 Feb 2017 05:32:34 -0500 |
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#!/usr/bin/env python """Filter a FASTA file with IDs from a tabular file, e.g. from BLAST. NOTE - This script is now OBSOLETE, having been replaced by a new verion which handles FASTA, FASTQ and SFF all in one. 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 tool is copyright 2010-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See accompanying text file for licence details (MIT license). """ import sys if "-v" in sys.argv or "--version" in sys.argv: print "v0.0.5" sys.exit(0) from galaxy_utils.sequence.fasta import fastaReader, fastaWriter # Parse Command Line try: tabular_file, cols_arg, in_file, out_positive_file, out_negative_file = sys.argv[1:] except ValueError: sys.exit("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: sys.exit("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 FASTA file based on IDs from tabular file 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() else: sys.exit("Neither output file requested") reader.close()