# HG changeset patch # User peterjc # Date 1307483018 14400 # Node ID 838b9bebfa3c475287f1b2c78d5ae6bd32dfe74c Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository diff -r 000000000000 -r 838b9bebfa3c tools/filters/seq_select_by_id.py --- /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 diff -r 000000000000 -r 838b9bebfa3c tools/filters/seq_select_by_id.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/seq_select_by_id.txt Tue Jun 07 17:43:38 2011 -0400 @@ -0,0 +1,78 @@ +Galaxy tool to select FASTA, FASTQ or SFF sequences by ID +========================================================= + +This tool is copyright 2011 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using Biopython library functions) to extract +sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given +by a column of a tabular file. The output order follows that of the tabular file, +and if there are duplicates in the tabular file, there will be duplicates in the +output sequence file. + +See also the sister tool to filter sequence files according to IDs from column(s) +of a tabular file, where the output order follows the sequence file, and any +duplicate IDs are ignored. + +There are just two files to install: + +* seq_select_by_id.py (the Python script) +* seq_select_by_id.xml (the Galaxy tool definition) + +The suggested location is in the Galaxy folder tools/filters next to the tool +for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +tool. One suggested location is in the filters section. Simply add the line: + + + +You will also need to install Biopython 1.54 or later. That's it. + + +History +======= + +v0.0.1 - Initial version. + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* + +Check this worked: + +$ tar -tzf seq_select_by_id.tar.gz +filter/seq_select_by_id.py +filter/seq_select_by_id.txt +filter/seq_select_by_id.xml + + +Licence (MIT/BSD style) +======================= + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. diff -r 000000000000 -r 838b9bebfa3c tools/filters/seq_select_by_id.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/seq_select_by_id.xml Tue Jun 07 17:43:38 2011 -0400 @@ -0,0 +1,51 @@ + + from a tabular file + +seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file + + + + + + + + + + + + + + + + + + + + + + + Bio + + + +**What it does** + +Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a +new sequence file (of the same format) containing only the records with identifiers +in the tabular file (in the order from the tabular file). + +WARNING: If you have any duplicates in the tabular file identifiers, you will get +duplicate sequences in the output. + +**Citation** + +This tool uses Biopython to read, write and index sequence files. If you use +this tool in scientific work leading to a publication, please cite the +Biopython application note (and Galaxy too of course): + +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. + + +