Mercurial > repos > peterjc > seq_select_by_id
diff tools/filters/seq_select_by_id.py @ 0:838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:43:38 -0400 |
parents | |
children | 50a8a6917a9c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/seq_select_by_id.py Tue Jun 07 17:43:38 2011 -0400 @@ -0,0 +1,126 @@ +#!/usr/bin/env python +"""Select FASTA, QUAL, FASTQ or SSF sequences by IDs from a tabular file. + +Takes five command line options, tabular filename, ID column number (using +one based counting), input filename, input type (e.g. FASTA or SFF) and the +output filename (same format as input sequence file). + +When selecting from an SFF file, any Roche XML manifest in the input file is +preserved in both output files. + +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 2011 by Peter Cock, The James Hutton Institute 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, col_arg, in_file, seq_format, out_file = sys.argv[1:] +except ValueError: + stop_err("Expected five arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) +try: + if col_arg.startswith("c"): + column = int(col_arg[1:])-1 + else: + column = int(col_arg)-1 +except ValueError: + stop_err("Expected column number, got %s" % cols_arg) + +if seq_format == "fastqcssanger": + stop_err("Colorspace FASTQ not supported.") +elif seq_format.lower() in ["sff", "fastq", "qual", "fasta"]: + seq_format = seq_format.lower() +elif seq_format.lower().startswith("fastq"): + #We don't care how the qualities are encoded + seq_format = "fastq" +elif seq_format.lower().startswith("qual"): + #We don't care what the scores are + seq_format = "qual" +else: + stop_err("Unrecognised file format %r" % seq_format) + + +try: + from Bio import SeqIO +except ImportError: + stop_err("Biopython 1.54 or later is required") + + +def parse_ids(tabular_file, col): + """Read tabular file and record all specified identifiers.""" + handle = open(tabular_file, "rU") + for line in handle: + if not line.startswith("#"): + yield line.rstrip("\n").split("\t")[col].strip() + handle.close() + +#Index the sequence file. +#If very big, could use SeqIO.index_db() to avoid memory bottleneck... +records = SeqIO.index(in_file, seq_format) +print "Indexed %i sequences" % len(records) + +if seq_format.lower()=="sff": + #Special case to try to preserve the XML manifest + 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 + in_handle.close() + + out_handle = open(out_file, "wb") + writer = SffWriter(out_handle, xml=manifest) + count = 0 + #This does have the overhead of parsing into SeqRecord objects, + #but doing the header and index at the low level is too fidly. + iterator = (records[name] for name in parse_ids(tabular_file, column)) + try: + count = writer.write_file(iterator) + except KeyError, err: + out_handle.close() + if name not in records: + stop_err("Identifier %s not found in sequence file" % name) + else: + raise err + out_handle.close() +else: + #Avoid overhead of parsing into SeqRecord objects, + #just re-use the original formatting from the input file. + out_handle = open(out_file, "w") + count = 0 + for name in parse_ids(tabular_file, column): + try: + out_handle.write(records.get_raw(name)) + except KeyError: + out_handle.close() + stop_err("Identifier %s not found in sequence file" % name) + count += 1 + out_handle.close() + +print "Selected %i sequences by ID" % count