# HG changeset patch
# User peterjc
# Date 1307481806 14400
# Node ID 10e963c79a454234514bb76ecc61a57d5be5d443
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
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
@@ -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()
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
@@ -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:
+
+
+
+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.
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
@@ -0,0 +1,75 @@
+
+ from a tabular file
+
+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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ output_choice_cond["output_choice"] != "neg"
+
+
+
+
+
+
+
+
+
+ output_choice_cond["output_choice"] != "pos"
+
+
+
+
+
+
+**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).
+
+
+