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113 lines
3.9 KiB
Python
Executable File
113 lines
3.9 KiB
Python
Executable File
#!/usr/bin/env python
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from __future__ import with_statement
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import sys
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from bx.bbi.bigwig_file import BigWigFile
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def die( message ):
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print >> sys.stderr, message
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sys.exit(1)
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def open_or_die( filename, mode='r', message=None ):
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if message is None:
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message = 'Error opening %s' % filename
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try:
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fh = open( filename, mode )
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except IOError as err:
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die( '%s: %s' % ( message, err.strerror ) )
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return fh
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class LocationFile( object ):
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def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ):
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self.filename = filename
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if comment_chars is None:
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self.comment_chars = ( '#' )
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else:
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self.comment_chars = tuple( comment_chars )
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self.delimiter = delimiter
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self.key_column = key_column
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self._map = {}
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self._populate_map()
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def _populate_map( self ):
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try:
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with open( self.filename ) as fh:
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line_number = 0
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for line in fh:
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line_number += 1
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line = line.rstrip( '\r\n' )
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if not line.startswith( self.comment_chars ):
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elems = line.split( self.delimiter )
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if len( elems ) <= self.key_column:
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die( 'Location file %s line %d: less than %d columns' % ( self.filename, line_number, self.key_column + 1 ) )
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else:
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key = elems.pop( self.key_column )
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if key in self._map:
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if self._map[key] != elems:
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die( 'Location file %s line %d: duplicate key "%s"' % ( self.filename, line_number, key ) )
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else:
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self._map[key] = elems
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except IOError as err:
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die( 'Error opening location file %s: %s' % ( self.filename, err.strerror ) )
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def get_values( self, key ):
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if key in self._map:
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rval = self._map[key]
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if len( rval ) == 1:
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return rval[0]
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else:
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return rval
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else:
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die( 'key "%s" not found in location file %s' % ( key, self.filename ) )
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def main():
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input_filename, output_filename, loc_filename, loc_key, chrom_col, start_col = sys.argv[1:]
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# open input, output, and bigwig files
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location_file = LocationFile( loc_filename )
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bigwig_filename = location_file.get_values( loc_key )
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bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file %s' % bigwig_filename )
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bw = BigWigFile( file=bwfh )
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ifh = open_or_die( input_filename, message='Error opening input file %s' % input_filename )
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ofh = open_or_die( output_filename, mode='w', message='Error opening output file %s' % output_filename )
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# make column numbers 0-based
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chrom_col = int( chrom_col ) - 1
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start_col = int( start_col ) - 1
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min_cols = max( chrom_col, start_col )
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# add score column to imput file
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line_number = 0
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for line in ifh:
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line_number += 1
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line = line.rstrip( '\r\n' )
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elems = line.split( '\t' )
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if len( elems ) > min_cols:
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chrom = elems[chrom_col].strip()
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# base-0 position in chrom
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start = int( elems[start_col] )
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score_list = bw.get( chrom, start, start + 1 )
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score_list_len = len( score_list )
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if score_list_len == 1:
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beg, end, score = score_list[0]
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score_val = '%1.3f' % score
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elif score_list_len == 0:
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score_val = 'NA'
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else:
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die( '%s line %d: chrom=%s, start=%d, score_list_len = %d' % ( input_filename, line_number, chrom, start, score_list_len ) )
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print >> ofh, '\t'.join( [line, score_val] )
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else:
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print >> ofh, line
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bwfh.close()
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ifh.close()
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ofh.close()
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if __name__ == "__main__":
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main()
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