Mercurial > repos > saket-choudhary > eqtl_tools
changeset 1:7265ecc0f879
Moving the files to proper hiererachy levels
author | Saket Choudhary<saketkc@gmail.com> |
---|---|
date | Sun, 16 Jun 2013 12:24:55 +0530 (2013-06-16) |
parents | 2cb13deb38ad |
children | c72dac728b06 |
files | panama.xml panama/panama.xml panama/panama_run.py panama/test-data/PANAMA_results.csv panama/test-data/sim_expr.csv panama/test-data/sim_snps.csv panama_run.py test-data/PANAMA_results.csv test-data/sim_expr.csv test-data/sim_snps.csv |
diffstat | 10 files changed, 1699 insertions(+), 1699 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/panama.xml Sun Jun 16 12:24:55 2013 +0530 @@ -0,0 +1,25 @@ +<tool id="panama1" name="panama" version="1.0.0"> + <requirements> + <requirement type="package">panama</requirement> + </requirements> + <description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description> + <command interpreter="python"> + panama_run.py --exp_data=$expression_data --snp_data=$snp_data --output1=$output1 + </command> + <inputs> + <param name="expression_data" type="data" format="text" label="Select Expression Data" /> + <param name="snp_data" type="data" format="text" label="Select SNP data" /> + </inputs> + <outputs> + <data name="output1" format="text" /> + </outputs> + <tests> + <test> + <param name="expression_data" value="sim_expr.csv" /> + <param name="snp_data" value="sim_snps.csv" /> + <output name="output1" file="PANAMA_results.csv" /> + </test> + </tests> + + +</tool>
--- a/panama/panama.xml Sun Jun 16 02:46:55 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -<tool id="panama1" name="panama" version="1.0.0"> - <requirements> - <requirement type="package">panama</requirement> - </requirements> - <description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description> - <command interpreter="python"> - panama_run.py --exp_data=$expression_data --snp_data=$snp_data --output1=$output1 - </command> - <inputs> - <param name="expression_data" type="data" format="text" label="Select Expression Data" /> - <param name="snp_data" type="data" format="text" label="Select SNP data" /> - </inputs> - <outputs> - <data name="output1" format="text" /> - </outputs> - <tests> - <test> - <param name="expression_data" value="sim_expr.csv" /> - <param name="snp_data" value="sim_snps.csv" /> - <output name="output1" file="PANAMA_results.csv" /> - </test> - </tests> - - -</tool>
--- a/panama/panama_run.py Sun Jun 16 02:46:55 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -#!/usr/bin/env python -""" -Run panama on expression and snp data -usage: panama_run.py [options] - --exp_data: Expression data CSV file - --snp_data: SNP data file - --output1: Output CSV dataset -""" - -import optparse, os, sys, subprocess, tempfile, shutil -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.cookbook import doc_optparse -from galaxy import util - -def stop_err( msg ): - sys.stderr.write( '%s\n' % msg ) - sys.exit() - - - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '', '--exp_data', dest='exp_data', help='The input Expression dataset') - parser.add_option( '', '--snp_data', dest='snp_data', help='The input snp dataset' ) - parser.add_option( '', '--output1', dest='output1', help='The output CSV dataset' ) - ( options, args ) = parser.parse_args() - - try: - tmp_dir = tempfile.mkdtemp() - panama_output_file_name = os.path.join(tmp_dir, "PANAMA_results.csv") - command = 'panama %s %s -d %s' %(options.exp_data,options.snp_data,tmp_dir) - print command - tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=command, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - #clean up temp files - print e - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - stop_err( 'Error opening panama') - # Move tmp_aligns_file_name to our output dataset location - shutil.move( panama_output_file_name, options.output1 ) - #clean up temp files - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - # check that there are results in the output file - if os.path.getsize( options.output1 ) > 0: - sys.stdout.write( 'PANAM results generated' ) - else: - stop_err( 'Error generating PANAMA results' ) - -if __name__=="__main__": __main__()
--- a/panama/test-data/PANAMA_results.csv Sun Jun 16 02:46:55 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,401 +0,0 @@ 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--- a/panama/test-data/sim_expr.csv Sun Jun 16 02:46:55 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,801 +0,0 @@ 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--- a/panama/test-data/sim_snps.csv Sun Jun 16 02:46:55 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,401 +0,0 @@ -,Sample0,Sample1,Sample2,Sample3,Sample4,Sample5,Sample6,Sample7,Sample8,Sample9,Sample10,Sample11,Sample12,Sample13,Sample14,Sample15,Sample16,Sample17,Sample18,Sample19,Sample20,Sample21,Sample22,Sample23,Sample24,Sample25,Sample26,Sample27,Sample28,Sample29,Sample30,Sample31,Sample32,Sample33,Sample34,Sample35,Sample36,Sample37,Sample38,Sample39,Sample40,Sample41,Sample42,Sample43,Sample44,Sample45,Sample46,Sample47,Sample48,Sample49,Sample50,Sample51,Sample52,Sample53,Sample54,Sample55,Sample56,Sample57,Sample58,Sample59,Sample60,Sample61,Sample62,Sample63,Sample64,Sample65,Sample66,Sample67,Sample68,Sample69,Sample70,Sample71,Sample72,Sample73,Sample74,Sample75,Sample76,Sample77,Sample78,Sample79,Sample80,Sample81,Sample82,Sample83,Sample84,Sample85,Sample86,Sample87,Sample88,Sample89,Sample90,Sample91,Sample92,Sample93,Sample94,Sample95,Sample96,Sample97,Sample98,Sample99,Sample100,Sample101,Sample102,Sample103,Sample104,Sample105,Sample106,Sample107,Sample108 -SNP0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0 -SNP1,1.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0 -SNP2,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP3,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP4,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP5,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP6,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP7,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP8,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP9,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP10,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP11,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP12,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP13,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP14,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0 -SNP15,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP16,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP17,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP18,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP19,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP20,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP21,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP22,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP23,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP24,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP25,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP26,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP27,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP28,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP29,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 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-SNP34,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP35,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP36,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP37,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP38,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP39,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 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-SNP50,1.0,1.0,0.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 -SNP51,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0 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-SNP218,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0 -SNP219,0.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0 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-SNP260,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0 -SNP261,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0 -SNP262,1.0,0.0,1.0,0.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0 -SNP263,1.0,0.0,1.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,1.0,1.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,1.0,0.0,1.0,1.0,0.0,1.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,1.0,0.0,0.0,0.0,1.0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/panama_run.py Sun Jun 16 12:24:55 2013 +0530 @@ -0,0 +1,71 @@ +#!/usr/bin/env python +""" +Run panama on expression and snp data +usage: panama_run.py [options] + --exp_data: Expression data CSV file + --snp_data: SNP data file + --output1: Output CSV dataset +""" + +import optparse, os, sys, subprocess, tempfile, shutil +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse +from galaxy import util + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + + + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '', '--exp_data', dest='exp_data', help='The input Expression dataset') + parser.add_option( '', '--snp_data', dest='snp_data', help='The input snp dataset' ) + parser.add_option( '', '--output1', dest='output1', help='The output CSV dataset' ) + ( options, args ) = parser.parse_args() + + try: + tmp_dir = tempfile.mkdtemp() + panama_output_file_name = os.path.join(tmp_dir, "PANAMA_results.csv") + command = 'panama %s %s -d %s' %(options.exp_data,options.snp_data,tmp_dir) + print command + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + #clean up temp files + print e + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + stop_err( 'Error opening panama') + # Move tmp_aligns_file_name to our output dataset location + shutil.move( panama_output_file_name, options.output1 ) + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + # check that there are results in the output file + if os.path.getsize( options.output1 ) > 0: + sys.stdout.write( 'PANAM results generated' ) + else: + stop_err( 'Error generating PANAMA results' ) + +if __name__=="__main__": __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PANAMA_results.csv Sun Jun 16 12:24:55 2013 +0530 @@ -0,0 +1,401 @@ 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sim_expr.csv Sun Jun 16 12:24:55 2013 +0530 @@ -0,0 +1,801 @@ 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