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1 #!/usr/bin/env python
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2 """
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3 Converts BAM data to sorted SAM data.
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4 usage: bam_to_sam.py [options]
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5 --input1: SAM file to be converted
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6 --output1: output dataset in bam format
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7 """
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8
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9 import optparse, os, sys, subprocess, tempfile, shutil
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10 from galaxy import eggs
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11 import pkg_resources; pkg_resources.require( "bx-python" )
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12 from bx.cookbook import doc_optparse
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13 #from galaxy import util
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14
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15 def stop_err( msg ):
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16 sys.stderr.write( '%s\n' % msg )
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17 sys.exit()
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18
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19 def __main__():
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20 #Parse Command Line
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21 parser = optparse.OptionParser()
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22 parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
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23 parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
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24 parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
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25 ( options, args ) = parser.parse_args()
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26
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27 # output version # of tool
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28 try:
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29 tmp = tempfile.NamedTemporaryFile().name
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30 tmp_stdout = open( tmp, 'wb' )
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31 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
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32 tmp_stdout.close()
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33 returncode = proc.wait()
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34 stdout = None
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35 for line in open( tmp_stdout.name, 'rb' ):
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36 if line.lower().find( 'version' ) >= 0:
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37 stdout = line.strip()
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38 break
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39 if stdout:
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40 sys.stdout.write( 'Samtools %s\n' % stdout )
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41 else:
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42 raise Exception
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43 except:
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44 sys.stdout.write( 'Could not determine Samtools version\n' )
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45
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46 tmp_dir = tempfile.mkdtemp()
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47
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48 try:
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49 # exit if input file empty
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50 if os.path.getsize( options.input1 ) == 0:
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51 raise Exception, 'Initial BAM file empty'
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52 # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
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53 # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
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54 # into memory ( controlled by option -m ).
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55 tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
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56 tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
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57 tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
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58 tmp_sorted_aligns_file.close()
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59 command = 'samtools sort %s %s' % ( options.input1, tmp_sorted_aligns_file_base )
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60 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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61 tmp_stderr = open( tmp, 'wb' )
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62 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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63 returncode = proc.wait()
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64 tmp_stderr.close()
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65 # get stderr, allowing for case where it's very large
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66 tmp_stderr = open( tmp, 'rb' )
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67 stderr = ''
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68 buffsize = 1048576
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69 try:
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70 while True:
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71 stderr += tmp_stderr.read( buffsize )
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72 if not stderr or len( stderr ) % buffsize != 0:
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73 break
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74 except OverflowError:
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75 pass
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76 tmp_stderr.close()
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77 if returncode != 0:
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78 raise Exception, stderr
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79 # exit if sorted BAM file empty
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80 if os.path.getsize( tmp_sorted_aligns_file_name) == 0:
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81 raise Exception, 'Intermediate sorted BAM file empty'
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82 except Exception, e:
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83 #clean up temp files
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84 if os.path.exists( tmp_dir ):
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85 shutil.rmtree( tmp_dir )
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86 stop_err( 'Error sorting alignments from (%s), %s' % ( options.input1, str( e ) ) )
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87
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88
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89 try:
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90 # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ).
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91 if options.header:
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92 view_options = "-h"
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93 else:
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94 view_options = ""
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95 command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name )
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96 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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97 tmp_stderr = open( tmp, 'wb' )
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98 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
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99 returncode = proc.wait()
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100 tmp_stderr.close()
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101 # get stderr, allowing for case where it's very large
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102 tmp_stderr = open( tmp, 'rb' )
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103 stderr = ''
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104 buffsize = 1048576
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105 try:
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106 while True:
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107 stderr += tmp_stderr.read( buffsize )
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108 if not stderr or len( stderr ) % buffsize != 0:
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109 break
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110 except OverflowError:
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111 pass
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112 tmp_stderr.close()
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113 if returncode != 0:
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114 raise Exception, stderr
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115 except Exception, e:
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116 #clean up temp files
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117 if os.path.exists( tmp_dir ):
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118 shutil.rmtree( tmp_dir )
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119 stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
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120 #clean up temp files
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121 if os.path.exists( tmp_dir ):
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122 shutil.rmtree( tmp_dir )
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123 # check that there are results in the output file
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124 if os.path.getsize( options.output1 ) > 0:
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125 sys.stdout.write( 'BAM file converted to SAM' )
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126 else:
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127 stop_err( 'The output file is empty, there may be an error with your input file.' )
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128
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129 if __name__=="__main__": __main__()
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