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annotate bismark_wrapper.py @ 25:a5faad9e4138 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
author bgruening
date Wed, 22 Aug 2018 08:09:23 -0400
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children b26a0df246fd
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25
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1 #!/usr/bin/env python
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2
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3 import argparse
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4 import fileinput
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5 import logging
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6 import math
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7 import os
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8 import shutil
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9 import subprocess
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10 import sys
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11 import tempfile
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12 from glob import glob
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15 def stop_err(logger, msg):
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16 logger.critical(msg)
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17 sys.exit(1)
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20 def log_subprocess_output(logger, pipe):
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21 for line in iter(pipe.readline, b''):
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22 logger.debug(line.decode().rstrip())
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25 def __main__():
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26 # Parse Command Line
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27 parser = argparse.ArgumentParser(description='Wrapper for the bismark bisulfite mapper.')
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28 parser.add_argument('-p', '--num-threads', dest='num_threads',
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29 type=int, default=4, help='Use this many threads to align reads. The default is 4.')
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31 # input options
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32 parser.add_argument('--own-file', dest='own_file', help='')
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33 parser.add_argument('-D', '--indexes-path', dest='index_path',
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34 help='Indexes directory; location of .ebwt and .fa files.')
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35 parser.add_argument('-O', '--output', dest='output')
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36
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37 parser.add_argument('--output-report-file', dest='output_report_file')
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38 parser.add_argument('--suppress-header', dest='suppress_header', action="store_true")
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39
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40 parser.add_argument('--mate-paired', dest='mate_paired', action='store_true', help='Reads are mate-paired',
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41 default=False)
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42
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43 parser.add_argument('-1', '--mate1', dest='mate1',
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44 help='The forward reads file in Sanger FASTQ or FASTA format.')
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45 parser.add_argument('-2', '--mate2', dest='mate2',
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46 help='The reverse reads file in Sanger FASTQ or FASTA format.')
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47 parser.add_argument('--sort-bam', dest='sort_bam', action="store_true")
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48
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49 parser.add_argument('--output-unmapped-reads', dest='output_unmapped_reads',
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50 help='Additional output file with unmapped reads (single-end).')
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51 parser.add_argument('--output-unmapped-reads-l', dest='output_unmapped_reads_l',
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52 help='File name for unmapped reads (left, paired-end).')
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53 parser.add_argument('--output-unmapped-reads-r', dest='output_unmapped_reads_r',
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54 help='File name for unmapped reads (right, paired-end).')
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55
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56 parser.add_argument('--output-suppressed-reads', dest='output_suppressed_reads',
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57 help='Additional output file with suppressed reads (single-end).')
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58 parser.add_argument('--output-suppressed-reads-l', dest='output_suppressed_reads_l',
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59 help='File name for suppressed reads (left, paired-end).')
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60 parser.add_argument('--output-suppressed-reads-r', dest='output_suppressed_reads_r',
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61 help='File name for suppressed reads (right, paired-end).')
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62 parser.add_argument('--stdout', dest='output_stdout',
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63 help='File name for the standard output of bismark.')
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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 parser.add_argument('--skip-reads', dest='skip_reads', type=int)
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73 parser.add_argument('--qupto', type=int)
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74
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75 # paired end options
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76 parser.add_argument('-I', '--minins', dest='min_insert')
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77 parser.add_argument('-X', '--maxins', dest='max_insert')
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78 parser.add_argument('--no-mixed', dest='no_mixed', action="store_true")
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79 parser.add_argument('--no-discordant', dest='no_discordant', action="store_true")
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80
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81 # parse general options
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82 # default 20
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83 parser.add_argument('--seed-len', dest='seed_len', type=int)
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84 # default 15
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85 parser.add_argument('--seed-extention-attempts', dest='seed_extention_attempts', type=int)
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86 # default 0
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87 parser.add_argument('--seed-mismatches', dest='seed_mismatches', type=int)
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88 # default 2
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89 parser.add_argument('--max-reseed', dest='max_reseed', type=int)
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90 """
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91 # default 70
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92 parser.add_argument( '--maqerr', dest='maqerr', type=int )
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93 """
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94
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95 """
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96 The number of megabytes of memory a given thread is given to store path
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97 descriptors in --best mode. Best-first search must keep track of many paths
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98 at once to ensure it is always extending the path with the lowest cumulative
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99 cost. Bowtie tries to minimize the memory impact of the descriptors, but
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100 they can still grow very large in some cases. If you receive an error message
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101 saying that chunk memory has been exhausted in --best mode, try adjusting
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102 this parameter up to dedicate more memory to the descriptors. Default: 512.
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103 """
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104 parser.add_argument('--chunkmbs', type=int, default=512)
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105
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106 args = parser.parse_args()
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107
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108 logger = logging.getLogger('bismark_wrapper')
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109 logger.setLevel(logging.DEBUG)
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110 ch = logging.StreamHandler(sys.stdout)
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111 if args.output_stdout:
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112 ch.setLevel(logging.WARNING)
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113 handler = logging.FileHandler(args.output_stdout)
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114 handler.setLevel(logging.DEBUG)
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115 logger.addHandler(handler)
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116 else:
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117 ch.setLevel(logging.DEBUG)
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118 logger.addHandler(ch)
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119
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120 # Create bismark index if necessary.
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121 index_dir = ""
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122 tmp_index_dir = None
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123 if args.own_file:
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124 logger.info("Create a temporary index with the offered files from the user. "
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125 "Utilizing the script: bismark_genome_preparation")
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126 tmp_index_dir = tempfile.mkdtemp()
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127 index_path = os.path.join(tmp_index_dir, '.'.join(os.path.split(args.own_file)[1].split('.')[:-1]))
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128 try:
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129 # Create a hard link pointing to args.own_file named 'index_path'.fa.
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130 os.symlink(args.own_file, index_path + '.fa')
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131 except Exception as e:
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132 if os.path.exists(tmp_index_dir):
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133 shutil.rmtree(tmp_index_dir)
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134 stop_err(logger, 'Error in linking the reference database!\n%s' % e)
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135 # bismark_genome_preparation needs the complete path to the folder in which the database is stored
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136 cmd_index = ['bismark_genome_preparation', '--bowtie2', tmp_index_dir]
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137 try:
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138 logger.info("Generating index with: '%s'", " ".join(cmd_index))
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139 process = subprocess.Popen(cmd_index, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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140 with process.stdout:
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141 log_subprocess_output(logger, process.stdout)
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142 exitcode = process.wait()
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143 if exitcode != 0:
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144 raise Exception(process.stderr)
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145 except Exception as e:
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146 if os.path.exists(tmp_index_dir):
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147 shutil.rmtree(tmp_index_dir)
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148 stop_err(logger, 'Error indexing reference sequence!\n%s' % e)
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149 index_dir = tmp_index_dir
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150 else:
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151 # bowtie path is the path to the index directory and the first path of the index file name
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152 index_dir = os.path.dirname(args.index_path)
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153
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154 # Build bismark command
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155 tmp_bismark_dir = tempfile.mkdtemp()
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156 output_dir = os.path.join(tmp_bismark_dir, 'results')
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157 cmd = ['bismark', '--bam', '--gzip', '--temp_dir', tmp_bismark_dir, '-o', output_dir, '--quiet']
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158
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159 if args.fasta:
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160 # the query input files (specified as mate1,mate2 or singles) are FastA
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161 cmd.append('--fasta')
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162 elif args.fastq:
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163 cmd.append('--fastq')
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164
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165 # alignment options
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166 if args.num_threads > 2:
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167 # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each
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168 cmd.extend(['-p', str(math.ceil(args.num_threads / 2))])
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169 if args.seed_mismatches:
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170 cmd.extend(['-N', str(args.seed_mismatches)])
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171 if args.seed_len:
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172 cmd.extend(['-L', str(args.seed_len)])
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173 if args.seed_extention_attempts:
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174 cmd.extend(['-D', str(args.seed_extention_attempts)])
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175 if args.max_reseed:
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176 cmd.extend(['-R', str(args.max_reseed)])
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177 if args.no_discordant:
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178 cmd.append('--no-discordant')
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179 if args.no_mixed:
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180 cmd.append('--no-mixed')
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181 if args.skip_reads:
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182 cmd.extend(['--skip', str(args.skip_reads)])
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183 if args.qupto:
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184 cmd.extend(['--upto', 'args.qupto'])
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185 if args.phred64:
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186 cmd.append('--phred64-quals')
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187 if args.suppress_header:
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188 cmd.append('--sam-no-hd')
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189 if args.output_unmapped_reads or (args.output_unmapped_reads_l and args.output_unmapped_reads_r):
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190 cmd.append('--un')
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191 if args.output_suppressed_reads or (args.output_suppressed_reads_l and args.output_suppressed_reads_r):
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192 cmd.append('--ambiguous')
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193
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194 cmd.append(index_dir)
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195 # Set up the reads
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196 if args.mate_paired:
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197 # paired-end reads library
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198 cmd.extend(['-1', args.mate1, '-2', args.mate2, '-I', str(args.min_insert), '-X', str(args.max_insert)])
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199 else:
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200 # single paired reads library
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201 cmd.append(args.single_paired)
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202
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203 # Run
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204 try:
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205 logger.info("Running bismark with: '%s'", " ".join(cmd))
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206 process = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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207 with process.stdout:
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208 log_subprocess_output(logger, process.stdout)
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209 exitcode = process.wait()
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210 if exitcode != 0:
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211 raise Exception(process.stderr)
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212 except Exception as e:
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213 stop_err(logger, 'Error in running bismark!\n%s' % e)
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214
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215 # collect and copy output files
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216 if args.output_report_file:
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217 output_report_file = open(args.output_report_file, 'w+')
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218 for line in fileinput.input(glob(os.path.join(output_dir, '*report.txt'))):
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219 output_report_file.write(line)
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220 output_report_file.close()
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221
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222 if args.output_suppressed_reads:
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223 if glob(os.path.join(output_dir, '*ambiguous_reads.txt')):
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224 shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads.txt'))[0], args.output_suppressed_reads)
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225 if args.output_suppressed_reads_l:
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226 if glob(os.path.join(output_dir, '*ambiguous_reads_1.txt')):
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227 shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads_1.txt'))[0], args.output_suppressed_reads_l)
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228 if args.output_suppressed_reads_r:
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229 if glob(os.path.join(output_dir, '*ambiguous_reads_2.txt')):
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230 shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads_2.txt'))[0], args.output_suppressed_reads_r)
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231
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232 if args.output_unmapped_reads:
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233 if glob(os.path.join(output_dir, '*unmapped_reads.txt')):
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234 shutil.move(glob(os.path.join(output_dir, '*unmapped_reads.txt'))[0], args.output_unmapped_reads)
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235 if args.output_unmapped_reads_l:
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236 if glob(os.path.join(output_dir, '*unmapped_reads_1.txt')):
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237 shutil.move(glob(os.path.join(output_dir, '*unmapped_reads_1.txt'))[0], args.output_unmapped_reads_l)
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238 if args.output_unmapped_reads_r:
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239 if glob(os.path.join(output_dir, '*unmapped_reads_2.txt')):
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240 shutil.move(glob(os.path.join(output_dir, '*unmapped_reads_2.txt'))[0], args.output_unmapped_reads_r)
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241
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242 try:
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243 # merge all bam files
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244 tmp_res = tempfile.NamedTemporaryFile(dir=output_dir).name
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245
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246 bam_files = glob(os.path.join(output_dir, '*.bam'))
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247 if len(bam_files) > 1:
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248 cmd = ['samtools', 'merge', '-@', str(args.num_threads), '-f', tmp_res, ' '.join(bam_files)]
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249 logger.info("Merging bams with: '%s'", cmd)
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250 process = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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251 with process.stdout:
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252 log_subprocess_output(logger, process.stdout)
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253 exitcode = process.wait()
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254 if exitcode != 0:
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255 raise Exception(process.stderr)
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256 else:
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257 tmp_res = bam_files[0]
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258
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259 bam_path = "%s" % tmp_res
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260
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261 if os.path.exists(bam_path):
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262 if args.sort_bam:
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263 cmd = ['samtools', 'sort', '-@', str(args.num_threads), bam_path, 'sorted_bam']
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264 logger.info("Sorting bam with: '%s'", cmd)
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265 process = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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266 with process.stdout:
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267 log_subprocess_output(logger, process.stdout)
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268 exitcode = process.wait()
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269 if exitcode != 0:
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270 raise Exception(process.stderr)
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271 shutil.move('sorted_bam.bam', args.output)
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272 else:
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273 shutil.move(bam_path, args.output)
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274 else:
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275 stop_err(logger, 'BAM file no found:\n%s' % bam_path)
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276
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277 except Exception as e:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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278 stop_err(logger, 'Error in merging bam files!\n%s' % e)
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279
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280 # Clean up temp dirs
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281 if tmp_index_dir and os.path.exists(tmp_index_dir):
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282 shutil.rmtree(tmp_index_dir)
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283 if os.path.exists(tmp_bismark_dir):
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284 shutil.rmtree(tmp_bismark_dir)
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285 if os.path.exists(output_dir):
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286 shutil.rmtree(output_dir)
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287
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288
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289 if __name__ == "__main__": __main__()