| Next changeset 1:b79caa511ba2 (2011-06-07) |
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Commit message:
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository |
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added:
tools/fastq/fastq_filter_by_id.py tools/fastq/fastq_filter_by_id.txt tools/fastq/fastq_filter_by_id.xml |
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| diff -r 000000000000 -r 10e963c79a45 tools/fastq/fastq_filter_by_id.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_filter_by_id.py Tue Jun 07 17:23:26 2011 -0400 |
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| @@ -0,0 +1,93 @@ +#!/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() |
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| diff -r 000000000000 -r 10e963c79a45 tools/fastq/fastq_filter_by_id.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_filter_by_id.txt Tue Jun 07 17:23:26 2011 -0400 |
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| @@ -0,0 +1,77 @@ +Galaxy tool to filter FASTQ sequences by ID +=========================================== + +This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using the Galaxy library functions) which +divides a FASTQ file in two, those sequences with or without an ID present in +the specified column(s) of a tabular file. Example uses include filtering based +on search results from a tool like NCBI BLAST before assembly. + +There are just two files to install: + +* fastq_filter_by_id.py (the Python script) +* fastq_filter_by_id.xml (the Galaxy tool definition) + +The suggested location is next to the similarly named fastq_filter.py and +fastq_filter.xml files which are included with Galaxy, i.e. in the Galaxy +folder tools/fastq + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer +the tool. The suggested location is next to the fastq_filter.xml entry. Simply +add the line: + +<tool file="fastq/fastq_filter_by_id.xml" /> + +That's it. + + +History +======= + +v0.0.1 - Initial verion (not publicly released) +v0.0.2 - Allow both, just pos or just neg output files + - Preserve the FASTQ variant in the XML wrapper + + +Developers +========== + +This script and similar versions for FASTA and SFF files are currently being +developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter + +For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +tar -czf fastq_filter_by_id.tar.gz tools/fastq/fastq_filter_by_id.* + +Check this worked: + +$ tar -tzf fastq_filter_by_id.tar.gz +fastq/fastq_filter_by_id.py +fastq/fastq_filter_by_id.txt +fastq/fastq_filter_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. |
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| diff -r 000000000000 -r 10e963c79a45 tools/fastq/fastq_filter_by_id.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_filter_by_id.xml Tue Jun 07 17:23:26 2011 -0400 |
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| @@ -0,0 +1,75 @@ +<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.2"> + <description>from a tabular file</description> + <command interpreter="python"> +fastq_filter_by_id.py $input_tabular $columns $input_fastq +#if $output_choice_cond.output_choice=="both" + $output_pos $output_neg +#elif $output_choice_cond.output_choice=="pos" + $output_pos - +#elif $output_choice_cond.output_choice=="neg" + - $output_neg +#end if + </command> + <inputs> + <param name="input_fastq" type="data" format="fastq" label="FASTQ file to filter on the identifiers"/> + <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTQ identifiers"/> + <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> + <validator type="no_options" message="Pick at least one column"/> + </param> + <conditional name="output_choice_cond"> + <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> + <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two FASTA files</option> + <option value="pos">Just positive matches (ID on list), as a single FASTA file</option> + <option value="neg">Just negative matches (ID not on list), as a single FASTA file</option> + </param> + <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> + <when value="both" /> + <when value="pos" /> + <when value="neg" /> + </conditional> + </inputs> + <outputs> + <data name="output_pos" format="fastq" label="With matched ID"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + <filter>output_choice_cond["output_choice"] != "neg"</filter> + </data> + <data name="output_neg" format="fastq" label="Without matched ID"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + <filter>output_choice_cond["output_choice"] != "pos"</filter> + </data> + </outputs> + <tests> + </tests> + <help> + +**What it does** + +By default it divides a FASTQ file in two, those sequences with or without an +ID present in the tabular file column(s) specified. You can opt to have a +single output file of just the matching records, or just the non-matching ones. + +Note that the order of sequences in the original FASTA file is preserved. +Also, if any sequences share an identifier, duplicates are not removed. + +**Example Usage** + +You may have performed some kind of contamination search, for example running +BLASTN against a database of cloning vectors or bacteria, giving you a tabular +file containing read identifiers. You could use this tool to extract only the +reads without BLAST matches (i.e. those which do not match your contaminant +database). + + </help> +</tool> |