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annotate bismark_wrapper.py @ 38:b2d0e92f81c2 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
author bgruening
date Thu, 22 Apr 2021 17:05:07 +0000
parents a81701137fa0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 #!/usr/bin/env python
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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(
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28 description="Wrapper for the bismark bisulfite mapper."
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29 )
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30 parser.add_argument(
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31 "-p",
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32 "--num-threads",
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33 dest="num_threads",
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34 type=int,
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35 default=4,
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36 help="Use this many threads to align reads. The default is 4.",
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37 )
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39 # input options
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40 parser.add_argument("--own-file", dest="own_file", help="")
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41 parser.add_argument(
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42 "-D",
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43 "--indexes-path",
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44 dest="index_path",
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45 help="Indexes directory; location of .ebwt and .fa files.",
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46 )
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47 parser.add_argument("-O", "--output", dest="output")
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48
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49 parser.add_argument("--output-report-file", dest="output_report_file")
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50 parser.add_argument(
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51 "--suppress-header", dest="suppress_header", action="store_true"
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52 )
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53
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54 parser.add_argument(
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55 "--mate-paired",
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56 dest="mate_paired",
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57 action="store_true",
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58 help="Reads are mate-paired",
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59 default=False,
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60 )
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61
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62 parser.add_argument(
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63 "-1",
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64 "--mate1",
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65 dest="mate1",
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66 help="The forward reads file in Sanger FASTQ or FASTA format.",
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67 )
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68 parser.add_argument(
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69 "-2",
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70 "--mate2",
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71 dest="mate2",
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72 help="The reverse reads file in Sanger FASTQ or FASTA format.",
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73 )
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74 parser.add_argument("--sort-bam", dest="sort_bam", action="store_true")
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75
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76 parser.add_argument(
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77 "--output-unmapped-reads",
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78 dest="output_unmapped_reads",
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79 help="Additional output file with unmapped reads (single-end).",
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80 )
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81 parser.add_argument(
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82 "--output-unmapped-reads-l",
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83 dest="output_unmapped_reads_l",
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84 help="File name for unmapped reads (left, paired-end).",
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85 )
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86 parser.add_argument(
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87 "--output-unmapped-reads-r",
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88 dest="output_unmapped_reads_r",
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89 help="File name for unmapped reads (right, paired-end).",
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90 )
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91
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92 parser.add_argument(
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93 "--output-suppressed-reads",
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94 dest="output_suppressed_reads",
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95 help="Additional output file with suppressed reads (single-end).",
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96 )
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97 parser.add_argument(
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98 "--output-suppressed-reads-l",
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99 dest="output_suppressed_reads_l",
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100 help="File name for suppressed reads (left, paired-end).",
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101 )
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102 parser.add_argument(
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103 "--output-suppressed-reads-r",
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104 dest="output_suppressed_reads_r",
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105 help="File name for suppressed reads (right, paired-end).",
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106 )
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107 parser.add_argument(
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108 "--stdout",
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109 dest="output_stdout",
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110 help="File name for the standard output of bismark.",
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111 )
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112
38
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113 parser.add_argument(
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114 "--single-paired",
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115 dest="single_paired",
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116 help="The single-end reads file in Sanger FASTQ or FASTA format.",
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117 )
25
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118
38
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119 parser.add_argument(
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120 "--fastq", action="store_true", help="Query filetype is in FASTQ format"
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121 )
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122 parser.add_argument(
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123 "--fasta", action="store_true", help="Query filetype is in FASTA format"
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124 )
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125 parser.add_argument("--phred64-quals", dest="phred64", action="store_true")
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126 parser.add_argument(
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127 "--non_directional", dest="non_directional", action="store_true"
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128 )
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129 parser.add_argument("--pbat", dest="pbat", action="store_true")
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130
38
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131 parser.add_argument("--skip-reads", dest="skip_reads", type=int)
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132 parser.add_argument("--score-min", dest="score_min", type=str)
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133 parser.add_argument("--qupto", type=int)
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134
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135 # paired end options
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136 parser.add_argument("-I", "--minins", dest="min_insert")
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137 parser.add_argument("-X", "--maxins", dest="max_insert")
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138 parser.add_argument("--no-mixed", dest="no_mixed", action="store_true")
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139 parser.add_argument("--no-discordant", dest="no_discordant", action="store_true")
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140
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141 # parse general options
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142 # default 20
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143 parser.add_argument("--seed-len", dest="seed_len", type=int)
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144 # default 15
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145 parser.add_argument(
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146 "--seed-extention-attempts", dest="seed_extention_attempts", type=int
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147 )
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148 # default 0
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149 parser.add_argument("--seed-mismatches", dest="seed_mismatches", type=int)
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150 # default 2
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151 parser.add_argument("--max-reseed", dest="max_reseed", type=int)
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152
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153 """
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154 The number of megabytes of memory a given thread is given to store path
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155 descriptors in --best mode. Best-first search must keep track of many paths
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156 at once to ensure it is always extending the path with the lowest cumulative
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157 cost. Bowtie tries to minimize the memory impact of the descriptors, but
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158 they can still grow very large in some cases. If you receive an error message
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159 saying that chunk memory has been exhausted in --best mode, try adjusting
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160 this parameter up to dedicate more memory to the descriptors. Default: 512.
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161 """
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162 parser.add_argument("--chunkmbs", type=int, default=512)
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163
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164 args = parser.parse_args()
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165
38
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166 logger = logging.getLogger("bismark_wrapper")
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167 logger.setLevel(logging.DEBUG)
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168 ch = logging.StreamHandler(sys.stdout)
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169 if args.output_stdout:
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170 ch.setLevel(logging.WARNING)
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171 handler = logging.FileHandler(args.output_stdout)
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172 handler.setLevel(logging.DEBUG)
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173 logger.addHandler(handler)
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174 else:
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175 ch.setLevel(logging.DEBUG)
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176 logger.addHandler(ch)
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177
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178 # Create bismark index if necessary.
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179 index_dir = ""
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180 tmp_index_dir = None
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181 if args.own_file:
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182 logger.info(
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183 "Create a temporary index with the offered files from the user. "
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184 "Utilizing the script: bismark_genome_preparation"
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185 )
25
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186 tmp_index_dir = tempfile.mkdtemp()
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187 index_path = os.path.join(
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188 tmp_index_dir, ".".join(os.path.split(args.own_file)[1].split(".")[:-1])
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189 )
25
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190 try:
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191 # Create a hard link pointing to args.own_file named 'index_path'.fa.
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192 os.symlink(args.own_file, index_path + ".fa")
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193 except Exception as e:
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194 if os.path.exists(tmp_index_dir):
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195 shutil.rmtree(tmp_index_dir)
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196 stop_err(logger, "Error in linking the reference database!\n%s" % e)
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197 # bismark_genome_preparation needs the complete path to the folder in which the database is stored
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198 cmd_index = ["bismark_genome_preparation", "--bowtie2", tmp_index_dir]
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199 try:
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200 logger.info("Generating index with: '%s'", " ".join(cmd_index))
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201 process = subprocess.Popen(
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202 cmd_index, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
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203 )
25
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204 with process.stdout:
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205 log_subprocess_output(logger, process.stdout)
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206 exitcode = process.wait()
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207 if exitcode != 0:
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208 raise Exception(process.stderr)
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209 except Exception as e:
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210 if os.path.exists(tmp_index_dir):
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211 shutil.rmtree(tmp_index_dir)
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212 stop_err(logger, "Error indexing reference sequence!\n%s" % e)
25
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213 index_dir = tmp_index_dir
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214 else:
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215 # bowtie path is the path to the index directory and the first path of the index file name
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216 index_dir = os.path.dirname(args.index_path)
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217
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218 # Build bismark command
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219 tmp_bismark_dir = tempfile.mkdtemp()
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220 output_dir = os.path.join(tmp_bismark_dir, "results")
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221 cmd = [
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222 "bismark",
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223 "--bam",
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224 "--temp_dir",
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225 tmp_bismark_dir,
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226 "-o",
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227 output_dir,
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228 "--quiet",
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229 ]
34
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230 if not args.pbat:
38
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231 cmd.append("--gzip")
25
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232
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233 if args.fasta:
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234 # the query input files (specified as mate1,mate2 or singles) are FastA
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235 cmd.append("--fasta")
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236 elif args.fastq:
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237 cmd.append("--fastq")
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238
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239 # alignment options
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240 if args.num_threads > 2:
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241 # divide num_threads by 2 here since bismark will spawn 2 jobs with -p threads each
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242 cmd.extend(["-p", str(int(math.floor(args.num_threads / 2)))])
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243 if args.seed_mismatches:
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244 cmd.extend(["-N", str(args.seed_mismatches)])
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245 if args.seed_len:
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246 cmd.extend(["-L", str(args.seed_len)])
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247 if args.seed_extention_attempts:
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248 cmd.extend(["-D", str(args.seed_extention_attempts)])
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249 if args.max_reseed:
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250 cmd.extend(["-R", str(args.max_reseed)])
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251 if args.no_discordant:
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252 cmd.append("--no-discordant")
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253 if args.no_mixed:
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254 cmd.append("--no-mixed")
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255 if args.skip_reads:
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256 cmd.extend(["--skip", str(args.skip_reads)])
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257 if args.score_min:
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258 cmd.extend(["--score_min", str(args.score_min)])
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259 if args.qupto:
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260 cmd.extend(["--upto", "args.qupto"])
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261 if args.phred64:
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262 cmd.append("--phred64-quals")
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263 if args.non_directional:
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264 cmd.append("--non_directional")
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265 if args.pbat:
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266 cmd.append("--pbat")
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267 if args.suppress_header:
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268 cmd.append("--sam-no-hd")
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269 if args.output_unmapped_reads or (
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270 args.output_unmapped_reads_l and args.output_unmapped_reads_r
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271 ):
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272 cmd.append("--un")
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273 if args.output_suppressed_reads or (
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274 args.output_suppressed_reads_l and args.output_suppressed_reads_r
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275 ):
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276 cmd.append("--ambiguous")
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277
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278 cmd.append(index_dir)
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279 # Set up the reads
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280 if args.mate_paired:
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281 # paired-end reads library
38
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282 cmd.extend(
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283 [
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284 "-1",
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285 args.mate1,
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286 "-2",
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287 args.mate2,
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288 "-I",
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289 str(args.min_insert),
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290 "-X",
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291 str(args.max_insert),
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292 ]
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293 )
25
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294 else:
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295 # single paired reads library
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296 cmd.append(args.single_paired)
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297
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298 # Run
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299 try:
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300 logger.info("Running bismark with: '%s'", " ".join(cmd))
38
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301 process = subprocess.Popen(
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302 args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
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303 )
25
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304 with process.stdout:
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305 log_subprocess_output(logger, process.stdout)
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306 exitcode = process.wait()
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307 if exitcode != 0:
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308 raise Exception(process.stderr)
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309 except Exception as e:
38
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310 stop_err(logger, "Error in running bismark!\n%s" % e)
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311
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312 # collect and copy output files
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313 if args.output_report_file:
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314 output_report_file = open(args.output_report_file, "w+")
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315 for line in fileinput.input(glob(os.path.join(output_dir, "*report.txt"))):
25
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316 output_report_file.write(line)
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317 output_report_file.close()
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318
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319 if args.output_suppressed_reads:
38
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320 if glob(os.path.join(output_dir, "*ambiguous_reads.*")):
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321 shutil.move(
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322 glob(os.path.join(output_dir, "*ambiguous_reads.*"))[0],
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323 args.output_suppressed_reads,
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324 )
25
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325 if args.output_suppressed_reads_l:
38
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326 if glob(os.path.join(output_dir, "*ambiguous_reads_1.*")):
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327 shutil.move(
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328 glob(os.path.join(output_dir, "*ambiguous_reads_1.*"))[0],
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329 args.output_suppressed_reads_l,
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330 )
25
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331 if args.output_suppressed_reads_r:
38
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332 if glob(os.path.join(output_dir, "*ambiguous_reads_2.*")):
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333 shutil.move(
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334 glob(os.path.join(output_dir, "*ambiguous_reads_2.*"))[0],
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335 args.output_suppressed_reads_r,
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336 )
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337
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338 if args.output_unmapped_reads:
38
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339 if glob(os.path.join(output_dir, "*unmapped_reads.*")):
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340 shutil.move(
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341 glob(os.path.join(output_dir, "*unmapped_reads.*"))[0],
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342 args.output_unmapped_reads,
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343 )
25
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344 if args.output_unmapped_reads_l:
38
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345 if glob(os.path.join(output_dir, "*unmapped_reads_1.*")):
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346 shutil.move(
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347 glob(os.path.join(output_dir, "*unmapped_reads_1.*"))[0],
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348 args.output_unmapped_reads_l,
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349 )
25
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350 if args.output_unmapped_reads_r:
38
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351 if glob(os.path.join(output_dir, "*unmapped_reads_2.*")):
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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352 shutil.move(
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353 glob(os.path.join(output_dir, "*unmapped_reads_2.*"))[0],
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
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354 args.output_unmapped_reads_r,
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355 )
25
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356
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357 try:
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358 # merge all bam files
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359 tmp_res = tempfile.NamedTemporaryFile(dir=output_dir).name
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360
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
361 bam_files = glob(os.path.join(output_dir, "*.bam"))
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
362 if len(bam_files) > 1:
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
363 cmd = [
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
364 "samtools",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
365 "merge",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
366 "-@",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
367 str(args.num_threads),
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
368 "-f",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
369 tmp_res
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
370 ]
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
371 [cmd.append(x) for x in bam_files]
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
372 logger.info("Merging bams with: '%s'", cmd)
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
373 process = subprocess.Popen(
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
374 args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
375 )
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
376 with process.stdout:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
377 log_subprocess_output(logger, process.stdout)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
378 exitcode = process.wait()
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
379 if exitcode != 0:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
380 raise Exception(process.stderr)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
381 else:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
382 tmp_res = bam_files[0]
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
383
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
384 bam_path = "%s" % tmp_res
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
385
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
386 if os.path.exists(bam_path):
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
387 if args.sort_bam:
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
388 cmd = [
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
389 "samtools",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
390 "sort",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
391 "-@",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
392 str(args.num_threads),
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
393 bam_path,
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
394 "sorted_bam",
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
395 ]
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
396 logger.info("Sorting bam with: '%s'", cmd)
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
397 process = subprocess.Popen(
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
398 args=cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
399 )
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
400 with process.stdout:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
401 log_subprocess_output(logger, process.stdout)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
402 exitcode = process.wait()
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
403 if exitcode != 0:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
404 raise Exception(process.stderr)
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
405 shutil.move("sorted_bam.bam", args.output)
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
406 else:
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
407 shutil.move(bam_path, args.output)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
408 else:
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
409 stop_err(logger, "BAM file no found:\n%s" % bam_path)
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
410
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
411 except Exception as e:
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
412 stop_err(logger, "Error in merging bam files!\n%s" % e)
25
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
413
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
414 # Clean up temp dirs
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
415 if tmp_index_dir and os.path.exists(tmp_index_dir):
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
416 shutil.rmtree(tmp_index_dir)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
417 if os.path.exists(tmp_bismark_dir):
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
418 shutil.rmtree(tmp_bismark_dir)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
419 if os.path.exists(output_dir):
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
420 shutil.rmtree(output_dir)
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
421
a5faad9e4138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
bgruening
parents:
diff changeset
422
38
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
423 if __name__ == "__main__":
b2d0e92f81c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 8fdc76a99a9dcf34549898a208317607afd18798"
bgruening
parents: 35
diff changeset
424 __main__()