diff sam_bitwise_flag_filter.py @ 0:0b2424a404d9 draft default tip

Uploaded tool tarball.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_bitwise_flag_filter.py	Mon Aug 26 15:11:25 2013 -0400
@@ -0,0 +1,149 @@
+#!/usr/bin/env python
+# Refactored on 11/13/2010 by Kanwei Li
+
+import sys
+import optparse
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def main():
+    usage = """%prog [options]
+    
+options (listed below) default to 'None' if omitted
+    """
+    parser = optparse.OptionParser(usage=usage)
+    
+    parser.add_option(
+        '--0x0001','--is_paired',
+        choices = ( '0','1' ),
+        dest='is_paired',
+        metavar="<0|1>",
+        help='The read is paired in sequencing')
+
+    parser.add_option(
+        '--0x0002','--is_proper_pair',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_proper_pair',
+        help='The read is mapped in a proper pair')
+
+    parser.add_option(
+        '--0x0004','--is_unmapped',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_unmapped',
+        help='The query sequence itself is unmapped')
+
+    parser.add_option(
+        '--0x0008','--mate_is_unmapped',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='mate_is_unmapped',
+        help='The mate is unmapped')
+
+    parser.add_option(
+        '--0x0010','--query_strand',
+        dest='query_strand',
+        metavar="<0|1>",
+        choices = ( '0','1' ),
+        help='Strand of the query: 0 = forward, 1 = reverse.')
+
+    parser.add_option(
+        '--0x0020','--mate_strand',
+        dest='mate_strand',
+        metavar="<0|1>",
+        choices = ('0','1'),
+        help='Strand of the mate: 0 = forward, 1 = reverse.')
+
+    parser.add_option(
+        '--0x0040','--is_first',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_first',
+        help='The read is the first read in a pair')
+
+    parser.add_option(
+        '--0x0080','--is_second',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_second',
+        help='The read is the second read in a pair')
+
+    parser.add_option(
+        '--0x0100','--is_not_primary',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_not_primary',
+        help='The alignment for the given read is not primary')
+
+    parser.add_option(
+        '--0x0200','--is_bad_quality',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_bad_quality',
+        help='The read fails platform/vendor quality checks')
+
+    parser.add_option(
+        '--0x0400','--is_duplicate',
+        choices = ( '0','1' ),
+        metavar="<0|1>",
+        dest='is_duplicate',
+        help='The read is either a PCR or an optical duplicate')
+        
+    parser.add_option(
+        '-f','--input_sam_file',
+        metavar="INPUT_SAM_FILE",
+        dest='input_sam',
+        default = False,
+        help='Name of the SAM file to be filtered. STDIN is default')
+            
+    parser.add_option(
+        '-c','--flag_column',
+        dest='flag_col',
+        default = '2',
+        help='Column containing SAM bitwise flag. 1-based')
+
+    options, args = parser.parse_args()
+
+    if options.input_sam:
+		infile = open ( options.input_sam, 'r')
+    else:
+    	infile = sys.stdin
+        
+    opt_ary = [
+        options.is_paired,
+        options.is_proper_pair,
+        options.is_unmapped,
+        options.mate_is_unmapped,
+        options.query_strand,
+        options.mate_strand,
+        options.is_first,
+        options.is_second,
+        options.is_not_primary,
+        options.is_bad_quality,
+        options.is_duplicate
+    ]
+    
+    opt_map = { '0': False, '1': True }
+    used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None]
+    flag_col = int( options.flag_col ) - 1
+    
+    for line in infile:
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ) and not line.startswith( '@' ) :
+            fields = line.split( '\t' )
+            flags = int( fields[flag_col] )
+            
+            valid_line = True
+            for index, opt_bool in used_indices:
+                if bool(flags & 0x0001 << index) != opt_bool:
+                    valid_line = False
+                    break
+                    
+            if valid_line:
+                print line
+
+if __name__ == "__main__": main()
+