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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 fileinput
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5 from glob import glob
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6
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7 def stop_err( msg ):
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8 sys.stderr.write( "%s\n" % msg )
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9 sys.exit()
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10
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11 def __main__():
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12 #Parse Command Line
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13 parser = argparse.ArgumentParser(description='Wrapper for the bismark bisulfite mapper.')
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14 parser.add_argument( '-p', '--num-threads', dest='num_threads',
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15 type=int, default=4, help='Use this many threads to align reads. The default is 4.' )
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16
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17 parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )
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18
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19 parser.add_argument( '--bowtie2', action='store_true', default=False, help='Running bismark with bowtie2 and not with bowtie.' )
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20
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21 # input options
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22 parser.add_argument( '--own-file', dest='own_file', help='' )
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23 parser.add_argument( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' )
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24 parser.add_argument( '-O', '--output', dest='output' )
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25 parser.add_argument( '--output-report-file', dest='output_report_file' )
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26 parser.add_argument( '--suppress-header', dest='suppress_header', action="store_true" )
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27
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28 parser.add_argument( '--mate-paired', dest='mate_paired', action='store_true', help='Reads are mate-paired', default=False)
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29
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30
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31 parser.add_argument( '-1', '--mate1', dest='mate1',
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32 help='The forward reads file in Sanger FASTQ or FASTA format.' )
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33 parser.add_argument( '-2', '--mate2', dest='mate2',
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34 help='The reverse reads file in Sanger FASTQ or FASTA format.' )
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35
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36 parser.add_argument( '--output-unmapped-reads', dest='output_unmapped_reads',
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37 help='Additional output file with unmapped reads (single-end).' )
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38 parser.add_argument( '--output-unmapped-reads-l', dest='output_unmapped_reads_l',
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39 help='File name for unmapped reads (left, paired-end).' )
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40 parser.add_argument( '--output-unmapped-reads-r', dest='output_unmapped_reads_r',
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41 help='File name for unmapped reads (right, paired-end).' )
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42
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43
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44 parser.add_argument( '--output-suppressed-reads', dest='output_suppressed_reads',
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45 help='Additional output file with suppressed reads (single-end).' )
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46 parser.add_argument( '--output-suppressed-reads-l', dest='output_suppressed_reads_l',
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47 help='File name for suppressed reads (left, paired-end).' )
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48 parser.add_argument( '--output-suppressed-reads-r', dest='output_suppressed_reads_r',
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49 help='File name for suppressed reads (right, paired-end).' )
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50
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51
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52 parser.add_argument( '--single-paired', dest='single_paired',
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53 help='The single-end reads file in Sanger FASTQ or FASTA format.' )
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54
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55 parser.add_argument( '--fastq', action='store_true', help='Query filetype is in FASTQ format')
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56 parser.add_argument( '--fasta', action='store_true', help='Query filetype is in FASTA format')
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57 parser.add_argument( '--phred64-quals', dest='phred64', action="store_true" )
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58
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59
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60 parser.add_argument( '--skip-reads', dest='skip_reads', type=int )
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61 parser.add_argument( '--qupto', type=int)
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62
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63
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64 # paired end options
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65 parser.add_argument( '-I', '--minins', dest='min_insert' )
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66 parser.add_argument( '-X', '--maxins', dest='max_insert' )
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67 parser.add_argument( '--no-mixed', dest='no_mixed', action="store_true" )
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68 parser.add_argument( '--no-discordant', dest='no_discordant', action="store_true" )
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69
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70 #parse general options
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71 # default 20
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72 parser.add_argument( '--seed-len', dest='seed_len', type=int)
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73 # default 15
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74 parser.add_argument( '--seed-extention-attempts', dest='seed_extention_attempts', type=int )
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75 # default 0
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76 parser.add_argument( '--seed-mismatches', dest='seed_mismatches', type=int )
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77 # default 2
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78 parser.add_argument( '--max-reseed', dest='max_reseed', type=int )
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79 """
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80 # default 70
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81 parser.add_argument( '--maqerr', dest='maqerr', type=int )
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82 """
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83
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84 """
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85 The number of megabytes of memory a given thread is given to store path
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86 descriptors in --best mode. Best-first search must keep track of many paths
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87 at once to ensure it is always extending the path with the lowest cumulative
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88 cost. Bowtie tries to minimize the memory impact of the descriptors, but
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89 they can still grow very large in some cases. If you receive an error message
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90 saying that chunk memory has been exhausted in --best mode, try adjusting
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91 this parameter up to dedicate more memory to the descriptors. Default: 512.
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92 """
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93 parser.add_argument( '--chunkmbs', type=int, default=512 )
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94
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95 args = parser.parse_args()
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96
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97 # Create bismark index if necessary.
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98 index_dir = ""
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99 if args.own_file:
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100 """
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101 Create a temporary index with the offered files from the user.
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102 Utilizing the script: bismark_genome_preparation
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103 bismark_genome_preparation --bowtie2 hg19/
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104 """
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105 tmp_index_dir = tempfile.mkdtemp()
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106 index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( args.own_file )[1].split( '.' )[:-1] ) )
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107 try:
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108 """
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109 Create a hard link pointing to args.own_file named 'index_path'.fa.
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110 """
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111 os.symlink( args.own_file, index_path + '.fa' )
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112 except Exception, e:
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113 if os.path.exists( tmp_index_dir ):
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114 shutil.rmtree( tmp_index_dir )
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115 stop_err( 'Error in linking the reference database.\n' + str( e ) )
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116 # bismark_genome_preparation needs the complete path to the folder in which the database is stored
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117 if args.bowtie2:
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118 cmd_index = 'bismark_genome_preparation --bowtie2 %s ' % ( tmp_index_dir )
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119 else:
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120 cmd_index = 'bismark_genome_preparation %s ' % ( tmp_index_dir )
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121 if args.bismark_path:
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122 # add the path to the bismark perl scripts, that is needed for galaxy
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123 cmd_index = '%s/%s' % (args.bismark_path, cmd_index)
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124 try:
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125 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
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126 tmp_stderr = open( tmp, 'wb' )
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127 proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stdout=open(os.devnull, 'wb'), stderr=tmp_stderr.fileno() )
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128 returncode = proc.wait()
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129 tmp_stderr.close()
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130 # get stderr, allowing for case where it's very large
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131 tmp_stderr = open( tmp, 'rb' )
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132 stderr = ''
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133 buffsize = 1048576
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134 try:
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135 while True:
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136 stderr += tmp_stderr.read( buffsize )
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137 if not stderr or len( stderr ) % buffsize != 0:
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138 break
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139 except OverflowError:
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140 pass
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141 tmp_stderr.close()
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142 if returncode != 0:
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143 raise Exception, stderr
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144 except Exception, e:
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145 if os.path.exists( tmp_index_dir ):
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146 shutil.rmtree( tmp_index_dir )
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147 stop_err( 'Error indexing reference sequence\n' + str( e ) )
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148 index_dir = tmp_index_dir
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149 else:
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150 index_dir = args.index_path
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151
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152 # Build bismark command
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153 tmp_bismark_dir = tempfile.mkdtemp()
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154 output_dir = os.path.join( tmp_bismark_dir, 'results')
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155 cmd = 'bismark %(args)s --temp_dir %(tmp_bismark_dir)s -o %(output_dir)s --quiet %(genome_folder)s %(reads)s'
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156 if args.bismark_path:
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157 # add the path to the bismark perl scripts, that is needed for galaxy
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158 cmd = '%s/%s' % (args.bismark_path, cmd)
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159
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160 arguments = {
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161 'genome_folder': index_dir,
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162 'args': '',
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163 'tmp_bismark_dir': tmp_bismark_dir,
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164 'output_dir': output_dir,
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165 }
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166
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167 additional_opts = ''
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168 # Set up the reads
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169 if args.mate_paired:
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170 # paired-end reads library
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171 reads = '-1 %s ' % ( args.mate1 )
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172 reads += ' -2 %s ' % ( args.mate2 )
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173 additional_opts += ' -I %s -X %s ' % (args.min_insert, args.max_insert)
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174 else:
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175 # single paired reads library
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176 reads = ' %s ' % ( args.single_paired )
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177
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178
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179 if not args.bowtie2:
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180 # use bowtie specific options
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181 additional_opts += ' --best '
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182 if args.seed_mismatches:
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183 # --seedmms
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184 additional_opts += ' -n %s ' % args.seed_mismatches
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185 if args.seed_len:
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186 # --seedlen
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187 additional_opts += ' -l %s ' % args.seed_len
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188
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189 # alignment options
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190 if args.bowtie2:
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191 additional_opts += ' -p %s --bowtie2 ' % args.num_threads
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192 if args.seed_mismatches:
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193 additional_opts += ' -N %s ' % args.seed_mismatches
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194 if args.seed_len:
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195 additional_opts += ' -L %s ' % args.seed_len
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196 if args.seed_extention_attempts:
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197 additional_opts += ' -D %s ' % args.seed_extention_attempts
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198 if args.max_reseed:
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199 additional_opts += ' -R %s ' % args.max_reseed
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200 if args.no_discordant:
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201 additional_opts += ' --no-discordant '
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202 if args.no_mixed:
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203 additional_opts += ' --no-mixed '
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204 """
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205 if args.maqerr:
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206 additional_opts += ' --maqerr %s ' % args.maqerr
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207 """
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208 if args.skip_reads:
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209 additional_opts += ' --skip %s ' % args.skip_reads
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210 if args.qupto:
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211 additional_opts += ' --qupto %s ' % args.qupto
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212 if args.phred64:
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213 additional_opts += ' --phred64-quals '
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214 if args.suppress_header:
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215 additional_opts += ' --sam-no-hd '
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216 if args.output_unmapped_reads or ( args.output_unmapped_reads_l and args.output_unmapped_reads_r):
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217 additional_opts += ' --un '
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218 if args.output_suppressed_reads or ( args.output_suppressed_reads_l and args.output_suppressed_reads_r):
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219 additional_opts += ' --ambiguous '
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220
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221 arguments.update( {'args': additional_opts, 'reads': reads} )
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222
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223 # Final command:
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224 cmd = cmd % arguments
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225
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226 # Run
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227 try:
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228 tmp_out = tempfile.NamedTemporaryFile().name
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229 tmp_stdout = open( tmp_out, 'wb' )
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230 tmp_err = tempfile.NamedTemporaryFile().name
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231 tmp_stderr = open( tmp_err, 'wb' )
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232 proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
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233 returncode = proc.wait()
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234 tmp_stderr.close()
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235 # get stderr, allowing for case where it's very large
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236 tmp_stderr = open( tmp_err, 'rb' )
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237 stderr = ''
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238 buffsize = 1048576
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239 try:
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240 while True:
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241 stderr += tmp_stderr.read( buffsize )
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242 if not stderr or len( stderr ) % buffsize != 0:
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243 break
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244 except OverflowError:
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245 pass
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246 tmp_stdout.close()
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247 tmp_stderr.close()
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248 if returncode != 0:
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249 raise Exception, stderr
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250
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251 # TODO: look for errors in program output.
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252 except Exception, e:
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253 stop_err( 'Error in bismark:\n' + str( e ) )
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254
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255
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256 # collect and copy output files
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257 """
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258 if args.output_report_file:
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259 output_report_file = open(args.output_report_file, 'w+')
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260 for line in fileinput.input(glob( os.path.join( output_dir, '*.txt') )):
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261 output_report_file.write(line)
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262 output_report_file.close()
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263 """
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264
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265 if args.output_suppressed_reads:
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266 shutil.move( glob(os.path.join( output_dir, '*ambiguous_reads.txt'))[0], args.output_suppressed_reads )
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267 if args.output_suppressed_reads_l:
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268 shutil.move( glob(os.path.join( output_dir, '*ambiguous_reads_1.txt'))[0], args.output_suppressed_reads_l )
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269 if args.output_suppressed_reads_r:
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270 shutil.move( glob(os.path.join( output_dir, '*ambiguous_reads_2.txt'))[0], args.output_suppressed_reads_r )
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271
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272 if args.output_unmapped_reads:
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273 shutil.move( glob(os.path.join( output_dir, '*unmapped_reads.txt'))[0], args.output_unmapped_reads )
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274 if args.output_unmapped_reads_l:
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275 shutil.move( glob(os.path.join( output_dir, '*unmapped_reads_1.txt'))[0], args.output_unmapped_reads_l )
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276 if args.output_unmapped_reads_r:
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277 shutil.move( glob(os.path.join( output_dir, '*unmapped_reads_2.txt'))[0], args.output_unmapped_reads_r )
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278
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279 shutil.move( glob( os.path.join( output_dir, '*.sam'))[0] , args.output)
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280
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281 # Clean up temp dirs
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282 if args.own_file:
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283 if os.path.exists( tmp_index_dir ):
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284 shutil.rmtree( tmp_index_dir )
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285 if os.path.exists( tmp_bismark_dir ):
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286 shutil.rmtree( tmp_bismark_dir )
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287
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288 if __name__=="__main__": __main__()
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