assemblystats: assembly_stats

annotate assembly_stats_txt.py @ 0:67b2a782bcfc default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

author	konradpaszkiewicz
date	Tue, 07 Jun 2011 15:48:22 -0400
parents
children

rev	line source
0 67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 #!/usr/bin/env python
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 #Version 1.01 - bugs kindly corrected by Jan van Haarst
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3 import pkg_resources
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 import logging, os, string, sys, tempfile, glob, shutil, types, urllib
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 import shlex, subprocess
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 from optparse import OptionParser, OptionGroup
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7 from stat import *
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 log = logging.getLogger( __name__ )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12 assert sys.version_info[:2] >= ( 2, 4 )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 def stop_err( msg ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 sys.stderr.write( "%s\n" % msg )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	16 sys.exit()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	17
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	18 def __main__():
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19 #Parse Command Line
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20 s = 'assembly_stats_txt.py: argv = %s\n' % (sys.argv)
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 argcnt = len(sys.argv)
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22 html_file = sys.argv[1]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23 working_dir = sys.argv[2]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 type = sys.argv[3]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25 bucket = sys.argv[4]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26 input = sys.argv[5]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 stats = sys.argv[6]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28 sortedcontigs = sys.argv[7]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29 histogrampng = sys.argv[8]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30 summedcontigspng = sys.argv[9]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	31 histogramdata = sys.argv[10]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 summedcontigdata = sys.argv[11]
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	33 try: # for test - needs this done
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	34 os.makedirs(working_dir)
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	35 except Exception, e:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36 stop_err( 'Error running assembly_stats_txt.py ' + str( e ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 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)
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40 try:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	41 proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42 returncode = proc.wait()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 # get stderr, allowing for case where it's very large
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44 stderr = ''
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	45 buffsize = 1048576
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46 try:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47 while True:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	48 stderr += proc.stderr.read( buffsize )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	49 if not stderr or len( stderr ) % buffsize != 0:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	50 break
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	51 except OverflowError:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	52 pass
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	53 if returncode != 0:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	54 raise Exception, stderr
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	55 except Exception, e:
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	56 stop_err( 'Error running assembly_stats.py ' + str( e ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	57
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	58 stats_path = os.path.join(working_dir,'stats.txt')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	59 sorted_contigs_path = os.path.join(working_dir,'sorted_contigs.fa')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	60 histogram_png_path = os.path.join(working_dir,'histogram_bins.dat.png')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	61 summed_contigs_path = os.path.join(working_dir,'summed_contig_lengths.dat.png')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	62 histogram_data_path = os.path.join(working_dir,'histogram_bins.dat')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	63 summed_contigs_data_path = os.path.join(working_dir,'summed_contig_lengths.dat')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	64
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	65 out = open(stats,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66 for line in open( stats_path ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67 out.write( "%s" % (line) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 out.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	69
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	70 out = open(sortedcontigs,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71 for line in open(sorted_contigs_path ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	72 out.write( "%s" % (line) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	73 out.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 out = open(histogrampng,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76 for line in open(histogram_png_path ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77 out.write( "%s" % (line) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78 out.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	79
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	80 out = open(summedcontigspng,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	81 for line in open(summed_contigs_path ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	82 out.write( "%s" % (line) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83 out.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	85
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	86 out = open(histogramdata,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	87 for line in open(histogram_data_path ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	88 out.write( "%s" % (line) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89 out.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91 out = open(summedcontigdata,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92 for line in open(summed_contigs_data_path ):
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93 out.write( "%s" % (line) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94 out.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	99
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	100
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	102
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 # rval = ['<html><head><title>Assembly stats Galaxy Composite Dataset </title></head><p/>']
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105 # rval.append('<div>%s<p/></div>' % (cmdline) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	106 # rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107 # rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (stats_path,'stats.txt','stats.txt' ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108 # rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sorted_contigs_path,'sorted_contigs.fa','sorted_contigs.fa' ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109 # rval.append( '<li><a href="%s" type="image/png">%s </a>%s</li>' % (histogram_png_path,'histogram_bins.dat.png','histogram_bins.dat.png' ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	110 # 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' ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111 # rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (histogram_data_path,'histogram_bins.dat','histogram_bins.dat' ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112 # 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' ) )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	114
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	115 #
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	116 # rval.append( '</ul></div></html>' )
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117 # f = file(html_file,'w')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	118 # f.write("\n".join( rval ))
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119 # f.write('\n')
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120 # f.close()
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	121
67b2a782bcfc Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	122 if __name__ == "__main__": __main__()

Mercurial > repos > konradpaszkiewicz > assemblystats

annotate assembly_stats_txt.py @ 0:67b2a782bcfc default tip