[2] | 1 | #!/usr/bin/env python |
---|
| 2 | |
---|
| 3 | import sys |
---|
| 4 | import optparse |
---|
| 5 | |
---|
| 6 | def stop_err( msg ): |
---|
| 7 | sys.stderr.write( msg ) |
---|
| 8 | sys.exit() |
---|
| 9 | |
---|
| 10 | def main(): |
---|
| 11 | usage = """%prog [options] |
---|
| 12 | |
---|
| 13 | options (listed below) default to 'None' if omitted |
---|
| 14 | """ |
---|
| 15 | parser = optparse.OptionParser(usage=usage) |
---|
| 16 | |
---|
| 17 | parser.add_option( |
---|
| 18 | '--0x0001','--is_paired', |
---|
| 19 | choices = ( '0','1' ), |
---|
| 20 | dest='is_paired', |
---|
| 21 | metavar="<0|1>", |
---|
| 22 | help='The read is paired in sequencing') |
---|
| 23 | |
---|
| 24 | parser.add_option( |
---|
| 25 | '--0x0002','--is_proper_pair', |
---|
| 26 | choices = ( '0','1' ), |
---|
| 27 | metavar="<0|1>", |
---|
| 28 | dest='is_proper_pair', |
---|
| 29 | help='The read is mapped in a proper pair') |
---|
| 30 | |
---|
| 31 | parser.add_option( |
---|
| 32 | '--0x0004','--is_unmapped', |
---|
| 33 | choices = ( '0','1' ), |
---|
| 34 | metavar="<0|1>", |
---|
| 35 | dest='is_unmapped', |
---|
| 36 | help='The query sequence itself is unmapped') |
---|
| 37 | |
---|
| 38 | parser.add_option( |
---|
| 39 | '--0x0008','--mate_is_unmapped', |
---|
| 40 | choices = ( '0','1' ), |
---|
| 41 | metavar="<0|1>", |
---|
| 42 | dest='mate_is_unmapped', |
---|
| 43 | help='The mate is unmapped') |
---|
| 44 | |
---|
| 45 | parser.add_option( |
---|
| 46 | '--0x0010','--query_strand', |
---|
| 47 | dest='query_strand', |
---|
| 48 | metavar="<0|1>", |
---|
| 49 | choices = ( '0','1' ), |
---|
| 50 | help='Strand of the query: 0 = forward, 1 = reverse.') |
---|
| 51 | |
---|
| 52 | parser.add_option( |
---|
| 53 | '--0x0020','--mate_strand', |
---|
| 54 | dest='mate_strand', |
---|
| 55 | metavar="<0|1>", |
---|
| 56 | choices = ('0','1'), |
---|
| 57 | help='Strand of the mate: 0 = forward, 1 = reverse.') |
---|
| 58 | |
---|
| 59 | parser.add_option( |
---|
| 60 | '--0x0040','--is_first', |
---|
| 61 | choices = ( '0','1' ), |
---|
| 62 | metavar="<0|1>", |
---|
| 63 | dest='is_first', |
---|
| 64 | help='The read is the first read in a pair') |
---|
| 65 | |
---|
| 66 | parser.add_option( |
---|
| 67 | '--0x0080','--is_second', |
---|
| 68 | choices = ( '0','1' ), |
---|
| 69 | metavar="<0|1>", |
---|
| 70 | dest='is_second', |
---|
| 71 | help='The read is the second read in a pair') |
---|
| 72 | |
---|
| 73 | parser.add_option( |
---|
| 74 | '--0x0100','--is_not_primary', |
---|
| 75 | choices = ( '0','1' ), |
---|
| 76 | metavar="<0|1>", |
---|
| 77 | dest='is_not_primary', |
---|
| 78 | help='The alignment for the given read is not primary') |
---|
| 79 | |
---|
| 80 | parser.add_option( |
---|
| 81 | '--0x0200','--is_bad_quality', |
---|
| 82 | choices = ( '0','1' ), |
---|
| 83 | metavar="<0|1>", |
---|
| 84 | dest='is_bad_quality', |
---|
| 85 | help='The read fails platform/vendor quality checks') |
---|
| 86 | |
---|
| 87 | parser.add_option( |
---|
| 88 | '--0x0400','--is_duplicate', |
---|
| 89 | choices = ( '0','1' ), |
---|
| 90 | metavar="<0|1>", |
---|
| 91 | dest='is_duplicate', |
---|
| 92 | help='The read is either a PCR or an optical duplicate') |
---|
| 93 | |
---|
| 94 | parser.add_option( |
---|
| 95 | '-f','--input_sam_file', |
---|
| 96 | metavar="INPUT_SAM_FILE", |
---|
| 97 | dest='input_sam', |
---|
| 98 | default = False, |
---|
| 99 | help='Name of the SAM file to be filtered. STDIN is default') |
---|
| 100 | |
---|
| 101 | parser.add_option( |
---|
| 102 | '-c','--flag_column', |
---|
| 103 | dest='flag_col', |
---|
| 104 | default = '2', |
---|
| 105 | help='Column containing SAM bitwise flag. 1-based') |
---|
| 106 | |
---|
| 107 | parser.add_option( |
---|
| 108 | '-d','--debug', |
---|
| 109 | dest='debug', |
---|
| 110 | action='store_true', |
---|
| 111 | default = False, |
---|
| 112 | help='Print debugging info') |
---|
| 113 | |
---|
| 114 | options, args = parser.parse_args() |
---|
| 115 | |
---|
| 116 | if options.input_sam: |
---|
| 117 | infile = open ( options.input_sam, 'r') |
---|
| 118 | else: |
---|
| 119 | infile = sys.stdin |
---|
| 120 | |
---|
| 121 | option_values = { '0': False, '1': True, None: None } |
---|
| 122 | |
---|
| 123 | states = []; |
---|
| 124 | states.append( option_values[ options.is_paired ] ) |
---|
| 125 | states.append( option_values[ options.is_proper_pair ] ) |
---|
| 126 | states.append( option_values[ options.is_unmapped ] ) |
---|
| 127 | states.append( option_values[ options.mate_is_unmapped ] ) |
---|
| 128 | states.append( option_values[ options.query_strand ] ) |
---|
| 129 | states.append( option_values[ options.mate_strand ] ) |
---|
| 130 | states.append( option_values[ options.is_first ] ) |
---|
| 131 | states.append( option_values[ options.is_second ] ) |
---|
| 132 | states.append( option_values[ options.is_not_primary ] ) |
---|
| 133 | states.append( option_values[ options.is_bad_quality ] ) |
---|
| 134 | states.append( option_values[ options.is_duplicate ] ) |
---|
| 135 | |
---|
| 136 | for line in infile: |
---|
| 137 | line = line.rstrip( '\r\n' ) |
---|
| 138 | if line and not line.startswith( '#' ) and not line.startswith( '@' ) : |
---|
| 139 | fields = line.split( '\t' ) |
---|
| 140 | sam_states = [] |
---|
| 141 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0001 ) ) |
---|
| 142 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0002 ) ) |
---|
| 143 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0004 ) ) |
---|
| 144 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0008 ) ) |
---|
| 145 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0010 ) ) |
---|
| 146 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0020 ) ) |
---|
| 147 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0040 ) ) |
---|
| 148 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0080 ) ) |
---|
| 149 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0100 ) ) |
---|
| 150 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0200 ) ) |
---|
| 151 | sam_states.append( bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0400 ) ) |
---|
| 152 | |
---|
| 153 | joined_states = zip(states,sam_states) |
---|
| 154 | searchable_fields = [] |
---|
| 155 | |
---|
| 156 | for i in range( len( joined_states ) ): |
---|
| 157 | if joined_states[i][0] != None: |
---|
| 158 | searchable_fields.append( joined_states[ i ] ) |
---|
| 159 | |
---|
| 160 | valid_line = True |
---|
| 161 | |
---|
| 162 | for i in range( len( searchable_fields ) ): |
---|
| 163 | if searchable_fields[i][0] != searchable_fields[i][1]: |
---|
| 164 | valid_line = False |
---|
| 165 | |
---|
| 166 | if valid_line: |
---|
| 167 | print line |
---|
| 168 | if options.debug: |
---|
| 169 | for i in range( len( joined_states ) ): |
---|
| 170 | print i, joined_states[i][0], joined_states[i][1] |
---|
| 171 | |
---|
| 172 | # if skipped_lines > 0: |
---|
| 173 | # print 'Skipped %d invalid lines' % skipped_lines |
---|
| 174 | |
---|
| 175 | |
---|
| 176 | if __name__ == "__main__": main() |
---|
| 177 | |
---|