Mercurial > repos > bgruening > bismark

annotate bismark_methyl_extractor/bismark_methylation_extractor.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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2
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3 import argparse, os, shutil, subprocess, sys, tempfile, fileinput
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4 import zipfile
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5 import re
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6 from glob import glob
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7
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8 def stop_err( msg ):
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9 sys.stderr.write( "%s\n" % msg )
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10 sys.exit()
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11
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12 def zipper(dir, zip_file):
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13 output_files_regex = re.compile('^(Non_)?C[pH][GH]_.*')
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14 bedgraph_regex = re.compile('.*bedGraph.gz')
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15 zip = zipfile.ZipFile(zip_file, 'w', compression=zipfile.ZIP_DEFLATED)
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16 root_len = len(os.path.abspath(dir))
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17 for root, dirs, files in os.walk(dir):
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18 archive_root = os.path.abspath(root)[root_len:]
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19 for f in files:
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20 if re.search(output_files_regex, f) or re.search(bedgraph_regex, f):
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21 fullpath = os.path.join(root, f)
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22 archive_name = os.path.join(archive_root, f)
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23 zip.write(fullpath, archive_name, zipfile.ZIP_DEFLATED)
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24 zip.close()
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25 return zip_file
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26
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27 def build_genome_dir(genome_file):
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28 tmp_genome_dir = tempfile.mkdtemp(prefix='tmp')
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29 genome_path = os.path.join(tmp_genome_dir, '.'.join(os.path.split(genome_file)[1].split('.')[:-1]))
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30 try:
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31 """
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32 Create a hard link pointing to genome_file named 'genome_path'.fa.
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33 """
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34 os.symlink(genome_file, genome_path + '.fa')
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35 except Exception, e:
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36 if os.path.exists(tmp_genome_dir):
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37 shutil.rmtree(tmp_genome_dir)
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38 stop_err('Error in linking the reference database.\n' + str(e))
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39 return tmp_genome_dir
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40
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41 def __main__():
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42 #Parse Command Line
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43 parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')
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44
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45 # input options
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46 parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )
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47
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48 parser.add_argument( '--infile', help='Input file in SAM or BAM format.' )
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49 parser.add_argument( '--single-end', dest='single_end', action="store_true" )
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50 parser.add_argument( '--paired-end', dest='paired_end', action="store_true" )
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51
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52 parser.add_argument('--splitting_report', dest='splitting_report')
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53 parser.add_argument('--mbias_report', dest='mbias_report')
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54 parser.add_argument('--cytosine_report', dest="cytosine_report")
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55 parser.add_argument('--genome_file', dest="genome_file")
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56 parser.add_argument('--cx_context', action="store_true" )
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57
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58 parser.add_argument( '--comprehensive', action="store_true" )
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59 parser.add_argument( '--merge-non-cpg', dest='merge_non_cpg', action="store_true" )
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60 parser.add_argument( '--no-overlap', dest='no_overlap', action="store_true" )
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61 parser.add_argument( '--compress' )
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62 parser.add_argument('--ignore', dest='ignore', type=int)
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63 parser.add_argument('--ignore_r2', dest='ignore_r2', type=int)
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64 parser.add_argument('--ignore_3prime', dest='ignore_3prime', type=int)
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65 parser.add_argument('--ignore_3prime_r2', dest='ignore_3prime_r2', type=int)
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66
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67 args = parser.parse_args()
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68
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69 # Build methylation extractor command
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70 output_dir = tempfile.mkdtemp()
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71 cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'
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72 if args.bismark_path:
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73 # add the path to the bismark perl scripts, that is needed for galaxy
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74 cmd = os.path.join(args.bismark_path, cmd)
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75
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76 # Set up all options
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77 additional_opts = ''
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78 if args.single_end:
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79 additional_opts += ' --single-end '
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80 else:
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81 additional_opts += ' --paired-end '
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82 if args.no_overlap:
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83 additional_opts += ' --no_overlap '
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84 if args.ignore:
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85 additional_opts += ' --ignore %s ' % args.ignore
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86 if args.ignore_r2:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
87 additional_opts += ' --ignore_r2 %s ' % args.ignore_r2
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
88 if args.ignore_3prime:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
89 additional_opts += ' --ignore_3prime %s ' % args.ignore_3prime
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
90 if args.ignore_3prime_r2:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
91 additional_opts += ' --ignore_3prime_r2 %s ' % args.ignore_3prime_r2
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
92 if args.comprehensive:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
93 additional_opts += ' --comprehensive '
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
94 if args.merge_non_cpg:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
95 additional_opts += ' --merge_non_CpG '
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
96 if args.splitting_report:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
97 additional_opts += ' --report '
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
98 if args.cytosine_report:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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99 tmp_genome_dir = build_genome_dir(args.genome_file)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
100 if args.cx_context:
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bgruening
parents:
diff changeset
101 additional_opts += ' --bedgraph --CX_context --cytosine_report --CX_context --genome_folder %s ' % tmp_genome_dir
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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diff changeset
102 else:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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103 additional_opts += ' --bedgraph --cytosine_report --genome_folder %s ' % tmp_genome_dir
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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104
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bgruening
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105
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bgruening
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106 #detect BAM file, use samtools view if it is a bam file
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bgruening
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107 f = open (args.infile, 'rb')
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bgruening
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108 sig = f.read(4)
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bgruening
parents:
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109 f.close()
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bgruening
parents:
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110 if sig == '\x1f\x8b\x08\x04' :
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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111 #cmd = cmd % (output_dir, additional_opts, '-')
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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112 new_infilename = os.path.join(output_dir, 'submitted_bs_mapped_reads.sam')
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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113 new_sam = open(new_infilename, 'wb')
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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114 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:
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115 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:
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116 proc = subprocess.Popen(['samtools', 'view', args.infile], stdout=new_sam, stderr=tmp_stderr)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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117 new_sam.close()
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bgruening
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118 tmp_stderr.close()
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bgruening
parents:
diff changeset
119 if os.stat(tmp_err).st_size != 0:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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120 tmp_sterr = 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
121 error_msg = tmp_sterr.read()
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
122 tmp_sterr.close()
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bgruening
parents:
diff changeset
123 sys.exit("error: %s" % error_msg)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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124 cmd = cmd % (output_dir, additional_opts, new_infilename)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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125 else:
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
126 cmd = cmd % (output_dir, additional_opts, args.infile)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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127
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128 # Run
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bgruening
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129 try:
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130 tmp_out = tempfile.NamedTemporaryFile().name
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bgruening
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131 tmp_stdout = open( tmp_out, 'wb' )
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132 tmp_err = tempfile.NamedTemporaryFile().name
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133 tmp_stderr = open( tmp_err, 'wb' )
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bgruening
parents:
diff changeset
134 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
135 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
136 tmp_stderr.close()
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
137 # 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
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diff changeset
138 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
139 stderr = ''
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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140 buffsize = 1048576
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bgruening
parents:
diff changeset
141 try:
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bgruening
parents:
diff changeset
142 while True:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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143 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
144 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
145 break
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bgruening
parents:
diff changeset
146 except OverflowError:
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bgruening
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diff changeset
147 pass
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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148 tmp_stdout.close()
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parents:
diff changeset
149 tmp_stderr.close()
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parents:
diff changeset
150 if returncode != 0:
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bgruening
parents:
diff changeset
151 raise Exception, stderr
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parents:
diff changeset
152
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bgruening
parents:
diff changeset
153 # TODO: look for errors in program output.
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bgruening
parents:
diff changeset
154 except Exception, e:
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bgruening
parents:
diff changeset
155 stop_err( 'Error in bismark methylation extractor:\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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parents:
diff changeset
156
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bgruening
parents:
diff changeset
157 # collect and copy output files
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bgruening
parents:
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158 if args.compress:
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bgruening
parents:
diff changeset
159 zipper(output_dir, args.compress)
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parents:
diff changeset
160
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
161 # cytosine report
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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162 if args.cytosine_report:
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bgruening
parents:
diff changeset
163 if args.cx_context:
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bgruening
parents:
diff changeset
164 shutil.move( glob(os.path.join( output_dir, '*CX_report.txt'))[0], args.cytosine_report )
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parents:
diff changeset
165 else:
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bgruening
parents:
diff changeset
166 shutil.move(glob(os.path.join(output_dir, '*CpG_report.txt'))[0], args.cytosine_report)
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
167 # splitting report
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
168 if args.splitting_report:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff changeset
169 shutil.move( glob(os.path.join( output_dir, '*_splitting_report.txt'))[0], args.splitting_report )
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bgruening
parents:
diff changeset
170 if args.mbias_report:
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bgruening
parents:
diff changeset
171 shutil.move(glob(os.path.join(output_dir, '*M-bias.txt'))[0], args.mbias_report)
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parents:
diff changeset
172
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diff changeset
173
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parents:
diff changeset
174 #Clean up temp dirs
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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175 if os.path.exists( output_dir ):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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176 shutil.rmtree( output_dir )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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177 if args.cytosine_report:
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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178 if os.path.exists( tmp_genome_dir ):
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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179 shutil.rmtree( tmp_genome_dir )
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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180
fcadce4d9a06 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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181 if __name__=="__main__": __main__()