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annotate bismark_methylation_extractor.py @ 22:8c191acde702 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author bgruening
date Tue, 01 Aug 2023 11:42:10 +0000
parents 120b7b35e442
children
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1 #!/usr/bin/env python
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3 import argparse
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4 import logging
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5 import math
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6 import os
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7 import re
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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 import zipfile
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13 from glob import glob
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16 def stop_err(logger, msg):
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17 logger.critical(msg)
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18 sys.exit(1)
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21 def log_subprocess_output(logger, pipe):
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22 for line in iter(pipe.readline, b""):
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23 logger.debug(line.decode().rstrip())
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26 def zipper(dir, zip_file):
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27 output_files_regex = re.compile("^(Non_)?C[pH][GH]_.*")
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28 bedgraph_regex = re.compile(".*bedGraph.gz")
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29 zip = zipfile.ZipFile(zip_file, "w", compression=zipfile.ZIP_DEFLATED)
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30 root_len = len(os.path.abspath(dir))
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31 for root, dirs, files in os.walk(dir):
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32 archive_root = os.path.abspath(root)[root_len:]
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33 for f in files:
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34 if re.search(output_files_regex, f) or re.search(bedgraph_regex, f):
9bfe38410155 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 51299fa62f0566a4a897b1c149db564631282fff
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35 fullpath = os.path.join(root, f)
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36 archive_name = os.path.join(archive_root, f)
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37 zip.write(fullpath, archive_name, zipfile.ZIP_DEFLATED)
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38 zip.close()
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39 return zip_file
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42 def build_genome_dir(genome_file):
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43 tmp_genome_dir = tempfile.mkdtemp(prefix="tmp")
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44 genome_path = os.path.join(
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45 tmp_genome_dir, ".".join(os.path.split(genome_file)[1].split(".")[:-1])
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46 )
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47 try:
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48 # Create a hard link pointing to genome_file named 'genome_path'.fa.
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49 os.symlink(genome_file, genome_path + ".fa")
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50 except Exception as e:
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51 if os.path.exists(tmp_genome_dir):
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52 shutil.rmtree(tmp_genome_dir)
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53 stop_err("Error in linking the reference database!\n%s" % e)
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54 return tmp_genome_dir
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57 def __main__():
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58 # Parse Command Line
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59 parser = argparse.ArgumentParser(
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60 description="Wrapper for the bismark methylation caller."
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61 )
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63 # input options
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64 parser.add_argument("--infile", help="Input file in SAM or BAM format.")
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65 parser.add_argument("--single-end", dest="single_end", action="store_true")
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66 parser.add_argument("--paired-end", dest="paired_end", action="store_true")
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68 parser.add_argument("--multicore", dest="multicore", type=int, default=1)
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69 parser.add_argument("--splitting_report", dest="splitting_report")
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70 parser.add_argument("--mbias_report", dest="mbias_report")
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71 parser.add_argument("--cytosine_report", dest="cytosine_report")
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72 parser.add_argument("--coverage_file", dest="coverage_file")
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73
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74 parser.add_argument("--genome_file", dest="genome_file")
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75 parser.add_argument("--cx_context", action="store_true")
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76
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77 parser.add_argument("--comprehensive", action="store_true")
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78 parser.add_argument("--merge-non-cpg", dest="merge_non_cpg", action="store_true")
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79 parser.add_argument("--no-overlap", dest="no_overlap", action="store_true")
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80 parser.add_argument("--compress", dest="compress")
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81 parser.add_argument("--ignore", dest="ignore", type=int)
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82 parser.add_argument("--ignore_r2", dest="ignore_r2", type=int)
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83 parser.add_argument("--ignore_3prime", dest="ignore_3prime", type=int)
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84 parser.add_argument("--ignore_3prime_r2", dest="ignore_3prime_r2", type=int)
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85 parser.add_argument(
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86 "--log_report", dest="log_report", metavar="log_filename", type=str
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87 )
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88 args = parser.parse_args()
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89
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90 logger = logging.getLogger("bismark_methylation_extractor_wrapper")
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91 logger.setLevel(logging.DEBUG)
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92 ch = logging.StreamHandler(sys.stdout)
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93 if args.log_report:
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94 ch.setLevel(logging.WARNING)
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95 handler = logging.FileHandler(args.log_report)
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96 handler.setLevel(logging.DEBUG)
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97 logger.addHandler(handler)
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98 else:
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99 ch.setLevel(logging.DEBUG)
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100 logger.addHandler(ch)
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101
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102 # Build methylation extractor command
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103 output_dir = tempfile.mkdtemp()
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104 cmd = ["bismark_methylation_extractor", "--no_header", "-o", output_dir]
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105 # Set up all options
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106 if args.multicore > 3:
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107 # divide multicore by 3 here since bismark will spawn ~3 jobs.
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108 cmd.extend(["--multicore", str(int(math.floor(args.multicore / 3)))])
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109 if args.single_end:
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110 cmd.append("--single-end")
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111 else:
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112 cmd.append("--paired-end")
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113 if args.no_overlap:
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114 cmd.append("--no_overlap")
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115 if args.ignore:
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116 cmd.extend(["--ignore", str(args.ignore)])
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117 if args.ignore_r2:
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118 cmd.extend(["--ignore_r2", str(args.ignore_r2)])
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119 if args.ignore_3prime:
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120 cmd.extend(["--ignore_3prime", str(args.ignore_3prime)])
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121 if args.ignore_3prime_r2:
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122 cmd.extend(["--ignore_3prime_r2", str(args.ignore_3prime_r2)])
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123 if args.comprehensive:
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124 cmd.append("--comprehensive")
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125 if args.merge_non_cpg:
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126 cmd.append("--merge_non_CpG")
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127 if args.splitting_report:
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128 cmd.append("--report")
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129 tmp_genome_dir = None
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130 if args.cytosine_report:
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131 tmp_genome_dir = build_genome_dir(args.genome_file)
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132 if args.cx_context:
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133 cmd.extend(
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134 [
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135 "--bedGraph",
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136 "--CX_context",
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137 "--cytosine_report",
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138 "--genome_folder",
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139 tmp_genome_dir,
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140 ]
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141 )
8
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142 else:
21
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143 cmd.extend(
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144 ["--bedGraph", "--cytosine_report", "--genome_folder", tmp_genome_dir]
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145 )
8
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146
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147 cmd.append(args.infile)
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148
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149 # Run
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150 logger.info("Methylation extractor run with: '%s'", " ".join(cmd))
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151 prev_dir = os.getcwd()
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152 os.chdir(
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153 output_dir
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154 ) # needed due to a bug in bismark where the coverage file cannot be found
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155 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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156 with process.stdout:
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157 log_subprocess_output(logger, process.stdout)
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158 exitcode = process.wait()
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159 if exitcode != 0:
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160 stop_err(
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161 logger,
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162 "Bismark methylation extractor error (also check the log file if any)!\n%s"
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163 % process.stderr,
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164 )
8
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165 logger.info("Finished methylation extractor.")
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166 # collect and copy output files
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167 logger.debug("Zip output files to '%s'.", args.compress)
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168 os.chdir(prev_dir)
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169 zipper(output_dir, args.compress)
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170
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171 # cytosine report
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172 if args.cytosine_report:
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173 logger.debug("Collecting cytosine report.")
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174 if args.cx_context:
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175 shutil.move(
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176 glob(os.path.join(output_dir, "*CX_report.txt"))[0],
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177 args.cytosine_report,
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178 )
22
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179
8
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180 else:
21
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181 shutil.move(
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182 glob(os.path.join(output_dir, "*CpG_report.txt"))[0],
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183 args.cytosine_report,
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184 )
22
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185
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186 # coverage file
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187 if args.coverage_file:
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188 shutil.move(
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189 glob(os.path.join(output_dir, "*datbismark.cov.gz"))[0],
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190 args.coverage_file,
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191 )
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192
8
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193 # splitting report
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194 if args.splitting_report:
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195 logger.debug("Collecting splitting report.")
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196 shutil.move(
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197 glob(os.path.join(output_dir, "*_splitting_report.txt"))[0],
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198 args.splitting_report,
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199 )
8
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200 if args.mbias_report:
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201 logger.debug("Collecting M-Bias file.")
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202 shutil.move(glob(os.path.join(output_dir, "*M-bias.txt"))[0], args.mbias_report)
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203
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204 # Clean up temp dirs
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205 logger.debug("Cleanup temp dirs.")
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206 if os.path.exists(output_dir):
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207 shutil.rmtree(output_dir)
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208 if tmp_genome_dir and os.path.exists(tmp_genome_dir):
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209 shutil.rmtree(tmp_genome_dir)
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210 logger.info("Done.")
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211
21
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212
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213 if __name__ == "__main__":
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214 __main__()