Mercurial > repos > aaronpetkau > assemblystats
diff assembly_stats_txt.py @ 0:8d1c7f2a3f5c draft default tip
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| author | aaronpetkau |
|---|---|
| date | Sat, 04 Jul 2015 09:43:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/assembly_stats_txt.py Sat Jul 04 09:43:13 2015 -0400 @@ -0,0 +1,122 @@ +#!/usr/bin/env python +#Version 1.01 - bugs kindly corrected by Jan van Haarst +import pkg_resources +import logging, os, string, sys, tempfile, glob, shutil, types, urllib +import shlex, subprocess +from optparse import OptionParser, OptionGroup +from stat import * + + +log = logging.getLogger( __name__ ) + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + s = 'assembly_stats_txt.py: argv = %s\n' % (sys.argv) + argcnt = len(sys.argv) + html_file = sys.argv[1] + working_dir = sys.argv[2] + type = sys.argv[3] + bucket = sys.argv[4] + input = sys.argv[5] + stats = sys.argv[6] + sortedcontigs = sys.argv[7] + histogrampng = sys.argv[8] + summedcontigspng = sys.argv[9] + histogramdata = sys.argv[10] + summedcontigdata = sys.argv[11] + try: # for test - needs this done + os.makedirs(working_dir) + except Exception, e: + stop_err( 'Error running assembly_stats_txt.py ' + str( e ) ) + + + cmdline = '%s/fasta_summary.pl -i %s -t %s %s -o %s > /dev/null' % (os.path.dirname(sys.argv[0]),input, type, bucket, working_dir) + try: + proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) + returncode = proc.wait() + # get stderr, allowing for case where it's very large + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += proc.stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + if returncode != 0: + raise Exception, stderr + except Exception, e: + stop_err( 'Error running assembly_stats.py ' + str( e ) ) + + stats_path = os.path.join(working_dir,'stats.txt') + sorted_contigs_path = os.path.join(working_dir,'sorted_contigs.fa') + histogram_png_path = os.path.join(working_dir,'histogram_bins.dat.png') + summed_contigs_path = os.path.join(working_dir,'summed_contig_lengths.dat.png') + histogram_data_path = os.path.join(working_dir,'histogram_bins.dat') + summed_contigs_data_path = os.path.join(working_dir,'summed_contig_lengths.dat') + + out = open(stats,'w') + for line in open( stats_path ): + out.write( "%s" % (line) ) + out.close() + + out = open(sortedcontigs,'w') + for line in open(sorted_contigs_path ): + out.write( "%s" % (line) ) + out.close() + + out = open(histogrampng,'w') + for line in open(histogram_png_path ): + out.write( "%s" % (line) ) + out.close() + + out = open(summedcontigspng,'w') + for line in open(summed_contigs_path ): + out.write( "%s" % (line) ) + out.close() + + + out = open(histogramdata,'w') + for line in open(histogram_data_path ): + out.write( "%s" % (line) ) + out.close() + + out = open(summedcontigdata,'w') + for line in open(summed_contigs_data_path ): + out.write( "%s" % (line) ) + out.close() + + + + + + + + + +# rval = ['<html><head><title>Assembly stats Galaxy Composite Dataset </title></head><p/>'] +# rval.append('<div>%s<p/></div>' % (cmdline) ) +# rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') +# rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (stats_path,'stats.txt','stats.txt' ) ) +# rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sorted_contigs_path,'sorted_contigs.fa','sorted_contigs.fa' ) ) +# rval.append( '<li><a href="%s" type="image/png">%s </a>%s</li>' % (histogram_png_path,'histogram_bins.dat.png','histogram_bins.dat.png' ) ) +# rval.append( '<li><a href="%s" type="image/png">%s </a>%s</li>' % (summed_contigs_path,'summed_contig_lengths.dat.png','summed_contig_lengths.dat.png' ) ) +# rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (histogram_data_path,'histogram_bins.dat','histogram_bins.dat' ) ) +# rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (summed_contigs_data_path,'summed_contig_lengths.dat','summed_contig_lengths.dat' ) ) + + +# +# rval.append( '</ul></div></html>' ) +# f = file(html_file,'w') +# f.write("\n".join( rval )) +# f.write('\n') +# f.close() + +if __name__ == "__main__": __main__()