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