Mercurial > repos > greg > gregs
changeset 2:81a79b4a3f6f
Deleted selected fasta files
| author | greg |
|---|---|
| date | Tue, 21 Jun 2011 09:44:52 -0400 |
| parents | 2f3ae18f13ed |
| children | 6ad594db0143 |
| files | bam_to_bigwig/tools/fasta_tools/fasta_filter_by_id.py bam_to_bigwig/tools/fasta_tools/fasta_filter_by_id.txt bam_to_bigwig/tools/fasta_tools/fasta_filter_by_id.xml |
| diffstat | 3 files changed, 0 insertions(+), 271 deletions(-) [+] |
line wrap: on
line diff
--- a/bam_to_bigwig/tools/fasta_tools/fasta_filter_by_id.py Tue Jun 21 09:44:13 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,92 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA 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 0.0.3 of the script. -""" -import sys -from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - -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 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: - stop_err("Neither output file requested") -reader.close()
--- a/bam_to_bigwig/tools/fasta_tools/fasta_filter_by_id.txt Tue Jun 21 09:44:13 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,89 +0,0 @@ -Obsolete -======== - -This tool is now obsolete, having been replaced by a more general version -covering the FASTA, FASTQ and SFF sequence formats in a single tool. You -should only install this tool if you need to support existing workflows -which used it. - - -Galaxy tool to filter FASTA 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 FASTA 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, TMHMM or SignalP. - -There are just two files to install: - -* fasta_filter_by_id.py (the Python script) -* fasta_filter_by_id.xml (the Galaxy tool definition) - -The suggested location is next to the similarly named fasta_filter_by_length.py -and fasta_filter_by_length.xml files which are included with Galaxy, i.e. -in the Galaxy folder tools/fasta_tools - -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 fasta_filter_by_length.xml -entry. Simply add the line: - -<tool file="fasta_tools/fasta_filter_by_id.xml" /> - -That's it. - - -History -======= - -v0.0.1 - Initial version (not publicly released) -v0.0.2 - Allow both, just pos or just neg output files -v0.0.3 - Include FASTA in tool name -v0.0.4 - Deprecated, marked as hidden in the XML - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -This incorporates the previously used 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 fasta_filter_by_id.tar.gz tools/fasta_tools/fasta_filter_by_id.* - -Check this worked: - -$ tar -tzf fasta_filter_by_id.tar.gz -fasta_tools/fasta_filter_by_id.py -fasta_tools/fasta_filter_by_id.txt -fasta_tools/fasta_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.
--- a/bam_to_bigwig/tools/fasta_tools/fasta_filter_by_id.xml Tue Jun 21 09:44:13 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.4" hidden="true"> - <description>from a tabular file</description> - <command interpreter="python"> -fasta_filter_by_id.py $input_tabular $columns $input_fasta -#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_fasta" type="data" format="fasta" label="FASTA file to filter on the identifiers"/> - <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTA 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="fasta" label="With matched ID"> - <filter>output_choice_cond["output_choice"] != "neg"</filter> - </data> - <data name="output_neg" format="fasta" label="Without matched ID"> - <filter>output_choice_cond["output_choice"] != "pos"</filter> - </data> - </outputs> - <tests> - <!-- Can't get these unit tests to run, may be a Galaxy problem - <test> - <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> - <param name="columns" value="1" /> - <param name="output_choice" value="both" /> - <output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" /> - <output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" /> - </test> - <test> - <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> - <param name="columns" value="1" /> - <param name="output_choice" value="pos" /> - <output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" /> - </test> - <test> - <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> - <param name="columns" value="1" /> - <param name="output_choice" value="neg" /> - <output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" /> - </test> - --> - </tests> - <help> - -**Deprecated** - -This tool is now obsolete, and should not be used in future. It has been -replaced by a more general version covering FASTA, FASTQ and SFF in one -single tool. - -**What it does** - -By default it divides a FASTA 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** - -Given a FASTA file of proteins you might run a signal peptide search (e.g. -via the SignalP wrapper for Galaxy), then filtered these tabular results to -select just those with a signal peptide. You could then use this tool to get -a FASTA file of only the proteins with predicted signal peptides. - - </help> -</tool>