# HG changeset patch
# User gregory-minevich
# Date 1332805012 14400
# Node ID bc7cc93ef659af8908427ca943b4072e678330a7
# Parent  a3873bb68495273bda8aa17db0bd5486a6436620
Deleted selected files

diff -r a3873bb68495 -r bc7cc93ef659 ._checkSnpEffCandidates.py
Binary file ._checkSnpEffCandidates.py has changed
diff -r a3873bb68495 -r bc7cc93ef659 ._checkSnpEffCandidates.xml
Binary file ._checkSnpEffCandidates.xml has changed
diff -r a3873bb68495 -r bc7cc93ef659 checkSnpEffCandidates.py
--- a/checkSnpEffCandidates.py	Tue Mar 20 11:02:34 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/usr/bin/python
-
-import sys
-import optparse
-import csv
-import re
-
-def main():
-	parser = optparse.OptionParser()
-	parser.add_option('-s', '--snpeff_file', dest = 'snpeff_file', action = 'store', type = 'string', default = None, help = "Path to the snpEff file")
-	parser.add_option('-c', '--candidate_list', dest = 'candidate_list', action = 'store', type = 'string', default = None, help = "Two column tabular list of candidate Gene ID, Type")
-	parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")	
-	(options, args) = parser.parse_args()
-	
-	snpeff_file = options.snpeff_file
-	candidate_list = options.candidate_list
-
-	candidates = parse_candidate_list(candidate_list = candidate_list)
-	mark_snpeff_file(snpeff_file = snpeff_file, output = options.output, candidates = candidates)
-
-def skip_and_write_headers(writer = None, reader = None, i_file = None):
-	# count headers
-	comment = 0
-	while reader.next()[0].startswith('#'):
-		comment = comment + 1
-	
-	# skip and write headers
-	i_file.seek(0)
-	for i in range(0, comment):
-		row = reader.next()
-		writer.writerow(row)
-
-def parse_candidate_list(candidate_list = ""):
-	i_file = open(candidate_list, 'rU')
-	reader  = csv.reader(i_file, delimiter = '\t',)
-
-	candidates = {}
-	for row in reader:
-		gene_id = row[0]
-		gene_type = row[1]
-		candidates[gene_id] = gene_type
-
-	i_file.close()
-	
-	return candidates
-
-def mark_snpeff_file(snpeff_file = "", output = "", candidates = None):
-	i_file = open(snpeff_file, 'rU')
-	reader = csv.reader(i_file, delimiter = '\t')
-
-	o_file = open(output, 'wb')
-	writer = csv.writer(o_file, delimiter = '\t')
-
-	skip_and_write_headers(writer = writer, reader = reader, i_file = i_file)
-
-	for row in reader:
-		gene_id = row[9]
-		if gene_id in candidates:
-			gene_type = candidates[gene_id]
-			row.append(gene_type)
-		else:
-			row.append('')
-
-		writer.writerow(row)
-
-	o_file.close()
-	i_file.close()
-
-if __name__ == "__main__":
-    main()
diff -r a3873bb68495 -r bc7cc93ef659 checkSnpEffCandidates.xml
--- a/checkSnpEffCandidates.xml	Tue Mar 20 11:02:34 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<tool id="check_snpeff_candidates" name="Check snpEff Candidates">
-    <description>Marks up a snpEff output file with matches to a gene candidate list.</description>
-    <command interpreter="python">checkSnpEffCandidates.py -s $snpeff_file -c $candidate_list -o $output</command>
-    <inputs>
-        <param name="snpeff_file" type="data" format="tabular" label="SnpEff File" help="tabular output file from snpEff"/>
-        <param name="candidate_list" type="data" format="tabular" label="Candidate List" help="2 column list consisting of candidate genes and a description"/>
-    </inputs>
-    <outputs>
-        <data format="tabular" name="output" />
-    </outputs>
-    <requirements>
-        <requirement type="python-module">sys</requirement>
-        <requirement type="python-module">optparse</requirement>
-        <requirement type="python-module">csv</requirement>
-    </requirements>
-    <tests>
-	<param name="snpeff_file" value="" />
-	<param name="candidate_list" value="" />
-    </tests>
-    <help>
-
-**What it does:** 
-
-Indicates on a SnpEff output file which genes are found in a candidate list by comparing Gene IDs.  
-
-For a description of the snpEff variant annotation and effect prediction tool:
-
-http://snpeff.sourceforge.net
-
-------
-
-**Input:** 
-
-The candidate list should be in a tabular format with two columns: Gene ID and Gene Description (e.g. C55B7.12 and transcription_factor). The file should contain no headers.
-
-Useful candidate lists (e.g. transcription factors, genes expressed in neurons, transgene silencers, chromatin factors) are available on the Hobert Lab website:
-
-http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
-
-
-------
-
-**Citation:**
-
-This tool is part of the CloudMap package from the Hobert Lab. If you use this tool, please cite `Gregory Minevich, Danny Park, Richard J. Poole and Oliver Hobert CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__
-
-    .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
-
-
-    </help>
-</tool>