diff tools/filters/trimmer.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/trimmer.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,106 @@
+#!/usr/bin/env python
+
+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(
+        '-a','--ascii',
+        dest='ascii',
+        action='store_true',
+        default = False,
+        help='Use ascii codes to defined ignored beginnings instead of raw characters')
+        
+    parser.add_option(
+        '-q','--fastq',
+        dest='fastq',
+        action='store_true',
+        default = False,
+        help='The input data in fastq format. It selected the script skips every even line since they contain sequence ids')
+
+    parser.add_option(
+        '-i','--ignore',
+        dest='ignore',
+        help='A comma separated list on ignored beginnings (e.g., ">,@"), or its ascii codes (e.g., "60,42") if option -a is enabled')
+
+    parser.add_option(
+        '-s','--start',
+        dest='start',
+        default = '0',
+        help='Trim from beginning to here (1-based)')
+
+    parser.add_option(
+        '-e','--end',
+        dest='end',
+        default = '0',
+        help='Trim from here to the ned (1-based)')
+
+    parser.add_option(
+        '-f','--file',
+        dest='input_txt',
+        default = False,
+        help='Name of file to be chopped. STDIN is default')
+            
+    parser.add_option(
+        '-c','--column',
+        dest='col',
+        default = '0',
+        help='Column to chop. If 0 = chop the whole line')
+       
+
+    options, args = parser.parse_args()
+    invalid_starts = []
+
+    if options.input_txt:
+		infile = open ( options.input_txt, 'r')
+    else:
+    	infile = sys.stdin
+    	
+    if options.ignore and options.ignore != "None":
+        invalid_starts = options.ignore.split(',')
+        
+    if options.ascii and options.ignore and options.ignore != "None":
+        for i, item in enumerate( invalid_starts ):
+            invalid_starts[i] = chr( int( item ) )
+
+    col = int( options.col )
+ 
+    for i, line in enumerate( infile ):
+        line = line.rstrip( '\r\n' )
+        if line:
+            
+            if options.fastq and i % 2 == 0:
+                print line
+                continue
+                
+
+            if line[0] not in invalid_starts:
+                if col == 0:
+                    if int( options.end ) > 0:
+                        line = line[ int( options.start )-1 : int( options.end ) ]
+                    else:
+                        line = line[ int( options.start )-1 : ]
+                else:
+                    fields = line.split( '\t' )
+                    if col-1 > len( fields ):
+                        stop_err('Column %d does not exist. Check input parameters\n' % col)
+                        
+                    if int( options.end ) > 0:
+                        fields[col - 1] = fields[col - 1][ int( options.start )-1 : int( options.end ) ]
+                    else:
+                        fields[col - 1] = fields[col - 1][ int( options.start )-1 : ]
+                    line = '\t'.join(fields)
+            print line   
+
+if __name__ == "__main__": main()
+