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annotate bismark_mapping/bismark_wrapper.py @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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7
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1 #!/usr/bin/env python
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3 import argparse
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4 import os
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5 import shutil
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6 import subprocess
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7 import sys
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8 import shlex
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9 import tempfile
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10 import fileinput
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11 import fileinput
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12 from glob import glob
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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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18 def __main__():
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20 #Parse Command Line
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21 parser = argparse.ArgumentParser(description='Wrapper for the bismark bisulfite mapper.')
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22 parser.add_argument( '-p', '--num-threads', dest='num_threads',
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23 type=int, default=4, help='Use this many threads to align reads. The default is 4.' )
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25 parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )
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27 parser.add_argument( '--bowtie2', action='store_true', default=False, help='Running bismark with bowtie2 and not with bowtie.' )
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29 # input options
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30 parser.add_argument( '--own-file', dest='own_file', help='' )
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31 parser.add_argument( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' )
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32 parser.add_argument( '-O', '--output', dest='output' )
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33
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34
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35 parser.add_argument( '--output-report-file', dest='output_report_file' )
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36 parser.add_argument( '--suppress-header', dest='suppress_header', action="store_true" )
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37
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38 parser.add_argument( '--mate-paired', dest='mate_paired', action='store_true', help='Reads are mate-paired', default=False)
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39
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40
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41 parser.add_argument( '-1', '--mate1', dest='mate1',
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42 help='The forward reads file in Sanger FASTQ or FASTA format.' )
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43 parser.add_argument( '-2', '--mate2', dest='mate2',
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44 help='The reverse reads file in Sanger FASTQ or FASTA format.' )
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45 parser.add_argument( '--sort-bam', dest='sort_bam', action="store_true" )
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46
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47 parser.add_argument( '--output-unmapped-reads', dest='output_unmapped_reads',
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48 help='Additional output file with unmapped reads (single-end).' )
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49 parser.add_argument( '--output-unmapped-reads-l', dest='output_unmapped_reads_l',
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50 help='File name for unmapped reads (left, paired-end).' )
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51 parser.add_argument( '--output-unmapped-reads-r', dest='output_unmapped_reads_r',
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52 help='File name for unmapped reads (right, paired-end).' )
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53
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54
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55 parser.add_argument( '--output-suppressed-reads', dest='output_suppressed_reads',
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56 help='Additional output file with suppressed reads (single-end).' )
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57 parser.add_argument( '--output-suppressed-reads-l', dest='output_suppressed_reads_l',
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58 help='File name for suppressed reads (left, paired-end).' )
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59 parser.add_argument( '--output-suppressed-reads-r', dest='output_suppressed_reads_r',
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60 help='File name for suppressed reads (right, paired-end).' )
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61 parser.add_argument( '--stdout', dest='output_stdout',
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62 help='File name for the standard output of bismark.' )
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63
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64
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65 parser.add_argument( '--single-paired', dest='single_paired',
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66 help='The single-end reads file in Sanger FASTQ or FASTA format.' )
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67
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68 parser.add_argument( '--fastq', action='store_true', help='Query filetype is in FASTQ format')
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69 parser.add_argument( '--fasta', action='store_true', help='Query filetype is in FASTA format')
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70 parser.add_argument( '--phred64-quals', dest='phred64', action="store_true" )
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71
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72
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73 parser.add_argument( '--skip-reads', dest='skip_reads', type=int )
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74 parser.add_argument( '--qupto', type=int)
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75
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76
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77 # paired end options
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78 parser.add_argument( '-I', '--minins', dest='min_insert' )
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79 parser.add_argument( '-X', '--maxins', dest='max_insert' )
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80 parser.add_argument( '--no-mixed', dest='no_mixed', action="store_true" )
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81 parser.add_argument( '--no-discordant', dest='no_discordant', action="store_true" )
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82
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83 #parse general options
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84 # default 20
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85 parser.add_argument( '--seed-len', dest='seed_len', type=int)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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diff changeset
86 # default 15
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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diff changeset
87 parser.add_argument( '--seed-extention-attempts', dest='seed_extention_attempts', type=int )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
88 # default 0
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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89 parser.add_argument( '--seed-mismatches', dest='seed_mismatches', type=int )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
90 # default 2
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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91 parser.add_argument( '--max-reseed', dest='max_reseed', type=int )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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92 """
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bgruening
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diff changeset
93 # default 70
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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94 parser.add_argument( '--maqerr', dest='maqerr', type=int )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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95 """
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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96
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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97 """
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98 The number of megabytes of memory a given thread is given to store path
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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99 descriptors in --best mode. Best-first search must keep track of many paths
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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100 at once to ensure it is always extending the path with the lowest cumulative
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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101 cost. Bowtie tries to minimize the memory impact of the descriptors, but
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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102 they can still grow very large in some cases. If you receive an error message
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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103 saying that chunk memory has been exhausted in --best mode, try adjusting
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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104 this parameter up to dedicate more memory to the descriptors. Default: 512.
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105 """
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106 parser.add_argument( '--chunkmbs', type=int, default=512 )
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107
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108 args = parser.parse_args()
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109
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110 # Create bismark index if necessary.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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111 index_dir = ""
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112 if args.own_file:
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113 """
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114 Create a temporary index with the offered files from the user.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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115 Utilizing the script: bismark_genome_preparation
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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116 bismark_genome_preparation --bowtie2 hg19/
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117 """
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118 tmp_index_dir = tempfile.mkdtemp()
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119 index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( args.own_file )[1].split( '.' )[:-1] ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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120 try:
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121 """
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122 Create a hard link pointing to args.own_file named 'index_path'.fa.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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123 """
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124 os.symlink( args.own_file, index_path + '.fa' )
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125 except Exception, e:
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126 if os.path.exists( tmp_index_dir ):
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127 shutil.rmtree( tmp_index_dir )
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128 stop_err( 'Error in linking the reference database.\n' + str( e ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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129 # bismark_genome_preparation needs the complete path to the folder in which the database is stored
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130 if args.bowtie2:
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131 cmd_index = 'bismark_genome_preparation --bowtie2 %s ' % ( tmp_index_dir )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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132 else:
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133 cmd_index = 'bismark_genome_preparation %s ' % ( tmp_index_dir )
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134 if args.bismark_path:
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135 if os.path.exists(args.bismark_path):
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136 # add the path to the bismark perl scripts, that is needed for galaxy
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137 cmd_index = os.path.join(args.bismark_path, cmd_index)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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138 else:
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139 # assume the same directory as that script
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140 cmd_index = 'perl %s' % os.path.join(os.path.realpath(os.path.dirname(__file__)), cmd_index)
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141 try:
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142 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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143 tmp_stderr = open( tmp, 'wb' )
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144 proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stdout=open(os.devnull, 'wb'), stderr=tmp_stderr.fileno() )
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145 returncode = proc.wait()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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146 tmp_stderr.close()
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147 # get stderr, allowing for case where it's very large
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148 tmp_stderr = open( tmp, 'rb' )
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149 stderr = ''
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150 buffsize = 1048576
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151 try:
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152 while True:
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153 stderr += tmp_stderr.read( buffsize )
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154 if not stderr or len( stderr ) % buffsize != 0:
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155 break
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156 except OverflowError:
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157 pass
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158 tmp_stderr.close()
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159 if returncode != 0:
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160 raise Exception, stderr
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161 except Exception, e:
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162 if os.path.exists( tmp_index_dir ):
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163 shutil.rmtree( tmp_index_dir )
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164 stop_err( 'Error indexing reference sequence\n' + str( e ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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165 index_dir = tmp_index_dir
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166 else:
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167 # bowtie path is the path to the index directory and the first path of the index file name
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168 index_dir = os.path.dirname( args.index_path )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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169
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170 # Build bismark command
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171
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172 """
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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173 Bismark requires a large amount of temporary disc space. If that is not available, for example on a cluster you can hardcode the
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174 TMP to some larger space. It's not recommended but it works.
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175 """
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176 #tmp_bismark_dir = tempfile.mkdtemp( dir='/data/0/galaxy_db/tmp/' )
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177 tmp_bismark_dir = tempfile.mkdtemp()
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178 output_dir = os.path.join( tmp_bismark_dir, 'results')
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179 cmd = 'bismark %(args)s --bam --temp_dir %(tmp_bismark_dir)s --gzip -o %(output_dir)s --quiet %(genome_folder)s %(reads)s'
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180
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181 if args.fasta:
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182 # the query input files (specified as mate1,mate2 or singles) are FastA
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183 cmd = '%s %s' % (cmd, '--fasta')
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184 elif args.fastq:
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185 cmd = '%s %s' % (cmd, '--fastq')
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186
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187 if args.bismark_path:
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188 # add the path to the bismark perl scripts, that is needed for galaxy
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189 if os.path.exists(args.bismark_path):
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190 cmd = os.path.join(args.bismark_path, cmd)
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191 else:
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192 # assume the same directory as that script
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193 cmd = 'perl %s' % os.path.join(os.path.realpath(os.path.dirname(__file__)), cmd)
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194
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195 arguments = {
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196 'genome_folder': index_dir,
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197 'args': '',
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198 'tmp_bismark_dir': tmp_bismark_dir,
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199 'output_dir': output_dir,
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200 }
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201
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202 additional_opts = ''
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203 # Set up the reads
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204 if args.mate_paired:
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205 # paired-end reads library
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206 reads = '-1 %s ' % ( args.mate1 )
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207 reads += ' -2 %s ' % ( args.mate2 )
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208 additional_opts += ' -I %s -X %s ' % (args.min_insert, args.max_insert)
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209 else:
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210 # single paired reads library
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211 reads = ' %s ' % ( args.single_paired )
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212
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213
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214 if not args.bowtie2:
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215 # use bowtie specific options
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216 #additional_opts += ' --best ' # bug in bismark, --best is not available as option. Only --non-best, best-mode is activated by default
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217 if args.seed_mismatches:
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218 # --seedmms
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219 additional_opts += ' -n %s ' % args.seed_mismatches
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220 if args.seed_len:
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221 # --seedlen
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222 additional_opts += ' -l %s ' % args.seed_len
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223
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224 # alignment options
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225 if args.bowtie2:
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226 additional_opts += ' -p %s --bowtie2 ' % (int(args.num_threads/2)) #divides by 2 here since bismark will spawn 2 (original top and original bottom) jobs with -p threads each
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227 if args.seed_mismatches:
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228 additional_opts += ' -N %s ' % args.seed_mismatches
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229 if args.seed_len:
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230 additional_opts += ' -L %s ' % args.seed_len
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231 if args.seed_extention_attempts:
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232 additional_opts += ' -D %s ' % args.seed_extention_attempts
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233 if args.max_reseed:
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234 additional_opts += ' -R %s ' % args.max_reseed
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235 if args.no_discordant:
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236 additional_opts += ' --no-discordant '
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237 if args.no_mixed:
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238 additional_opts += ' --no-mixed '
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239 """
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240 if args.maqerr:
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241 additional_opts += ' --maqerr %s ' % args.maqerr
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242 """
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243 if args.skip_reads:
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244 additional_opts += ' --skip %s ' % args.skip_reads
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245 if args.qupto:
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246 additional_opts += ' --qupto %s ' % args.qupto
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247 if args.phred64:
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248 additional_opts += ' --phred64-quals '
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249 if args.suppress_header:
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250 additional_opts += ' --sam-no-hd '
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251 if args.output_unmapped_reads or ( args.output_unmapped_reads_l and args.output_unmapped_reads_r):
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252 additional_opts += ' --un '
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253 if args.output_suppressed_reads or ( args.output_suppressed_reads_l and args.output_suppressed_reads_r):
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254 additional_opts += ' --ambiguous '
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255
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256 arguments.update( {'args': additional_opts, 'reads': reads} )
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257
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258 # Final bismark command:
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259 cmd = cmd % arguments
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260 # Run
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diff changeset
261 try:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
262 tmp_out = tempfile.NamedTemporaryFile().name
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
263 tmp_stdout = open( tmp_out, 'wb' )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
264 tmp_err = tempfile.NamedTemporaryFile().name
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
265 tmp_stderr = open( tmp_err, 'wb' )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
266 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
267 returncode = proc.wait()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
268
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
269 if returncode != 0:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
270 tmp_stdout.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
271 tmp_stderr.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
272 # get stderr, allowing for case where it's very large
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
273 tmp_stderr = open( tmp_err, 'rb' )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
274 stderr = ''
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
275 buffsize = 1048576
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
276 try:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
277 while True:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
278 stderr += tmp_stderr.read( buffsize )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
279 if not stderr or len( stderr ) % buffsize != 0:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
280 break
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
281 except OverflowError:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
282 pass
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
283
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
284 raise Exception, stderr
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
285 tmp_stdout.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
286 tmp_stderr.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
287
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
288 # TODO: look for errors in program output.
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
289 except Exception, e:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
290 stop_err( 'Error in bismark:\n' + str( e ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
291
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
292 # collect and copy output files
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
293 if args.output_report_file:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
294 output_report_file = open(args.output_report_file, 'w+')
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
295 for line in fileinput.input(glob( os.path.join( output_dir, '*report.txt') )):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
296 output_report_file.write(line)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
297 output_report_file.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
298
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
299
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
300 if args.output_suppressed_reads:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
301 if glob(os.path.join( output_dir, '*ambiguous_reads.txt')):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
302 shutil.move( glob(os.path.join( output_dir, '*ambiguous_reads.txt'))[0], args.output_suppressed_reads )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
303 if args.output_suppressed_reads_l:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
304 if glob(os.path.join(output_dir, '*ambiguous_reads_1.txt')):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
305 shutil.move( glob(os.path.join( output_dir, '*ambiguous_reads_1.txt'))[0], args.output_suppressed_reads_l )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
306 if args.output_suppressed_reads_r:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
307 if glob(os.path.join(output_dir, '*ambiguous_reads_2.txt')):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
308 shutil.move( glob(os.path.join( output_dir, '*ambiguous_reads_2.txt'))[0], args.output_suppressed_reads_r )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
309
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
310 if args.output_unmapped_reads:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
311 if glob(os.path.join(output_dir, '*unmapped_reads.txt')):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
312 shutil.move( glob(os.path.join( output_dir, '*unmapped_reads.txt'))[0], args.output_unmapped_reads )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
313 if args.output_unmapped_reads_l:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
314 if glob(os.path.join(output_dir, '*unmapped_reads_1.txt')):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
315 shutil.move( glob(os.path.join( output_dir, '*unmapped_reads_1.txt'))[0], args.output_unmapped_reads_l )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
316 if args.output_unmapped_reads_r:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
317 if glob(os.path.join(output_dir, '*unmapped_reads_2.txt')):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
318 shutil.move( glob(os.path.join( output_dir, '*unmapped_reads_2.txt'))[0], args.output_unmapped_reads_r )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
319
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
320 try:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
321 """
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
322 merge all bam files
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
323 """
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
324 #tmp_out = tempfile.NamedTemporaryFile( dir=output_dir ).name
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
325 tmp_stdout = open( tmp_out, 'wab' )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
326 #tmp_err = tempfile.NamedTemporaryFile( dir=output_dir ).name
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
327 tmp_stderr = open( tmp_err, 'wab' )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
328
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
329 tmp_res = tempfile.NamedTemporaryFile( dir= output_dir).name
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
330
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
331 bam_files = glob( os.path.join( output_dir, '*.bam') )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
332 if len( bam_files ) > 1:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
333 cmd = 'samtools merge -@ %s -f %s %s ' % ( args.num_threads, tmp_res, ' '.join( bam_files ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
334
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
335 proc = subprocess.Popen( args=shlex.split( cmd ), stdout=subprocess.PIPE )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
336
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
337 returncode = proc.wait()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
338 tmp_stdout.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
339 tmp_stderr.close()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
340 if returncode != 0:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
341 raise Exception, open( tmp_stderr.name ).read()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
342 else:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
343 tmp_res = bam_files[0]
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
344
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
345 bam_path = "%s" % tmp_res
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
346
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
347 if os.path.exists( bam_path ):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
348 if args.sort_bam:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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349 cmd = 'samtools sort -@ %s %s sorted_bam' % (args.num_threads, bam_path)
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350 proc = subprocess.Popen( args=shlex.split( cmd ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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351 returncode = proc.wait()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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352 if returncode != 0:
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353 raise Exception("Error during '%s'" % cmd)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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354 shutil.move( 'sorted_bam.bam', args.output )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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355 else:
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356 shutil.move( bam_path, args.output )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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357 else:
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358 stop_err( 'BAM file no found:\n' + str( bam_path ) )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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359
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360
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361 # TODO: look for errors in program output.
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362 except Exception, e:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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363 stop_err( 'Error in merging bam files:\n' + str( e ) )
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364
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365
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366 if args.output_stdout:
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367 # copy the temporary saved stdout from bismark
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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368 shutil.move( tmp_out, args.output_stdout )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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369
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370 # Clean up temp dirs
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371 if args.own_file:
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372 if os.path.exists( tmp_index_dir ):
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373 shutil.rmtree( tmp_index_dir )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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374 if os.path.exists( tmp_bismark_dir ):
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375 shutil.rmtree( tmp_bismark_dir )
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376 if os.path.exists( output_dir ):
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377 shutil.rmtree( output_dir )
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378
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379 if __name__=="__main__": __main__()