Mercurial > repos > miller-lab > genome_diversity
view LocationFile.py @ 9:22fe0154fa54
added support for heterochromatic regions
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Tue, 10 Jul 2012 11:41:22 -0400 |
parents | 2c498d40ecde |
children |
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#!/usr/bin/env python import sys def die( message ): print >> sys.stderr, message sys.exit(1) def open_or_die( filename, mode='r', message=None ): if message is None: message = 'Error opening {0}'.format( filename ) try: fh = open( filename, mode ) except IOError, err: die( '{0}: {1}'.format( message, err.strerror ) ) return fh class LocationFile( object ): def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ): self.filename = filename if comment_chars is None: self.comment_chars = ( '#' ) else: self.comment_chars = tuple( comment_chars ) self.delimiter = delimiter self.key_column = key_column self._map = {} self._populate_map() def _populate_map( self ): try: with open( self.filename ) as fh: line_number = 0 for line in fh: line_number += 1 line = line.rstrip( '\r\n' ) if not line.startswith( self.comment_chars ): elems = line.split( self.delimiter ) if len( elems ) <= self.key_column: die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) ) else: key = elems.pop( self.key_column ) if key in self._map: if self._map[key] != elems: die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) ) else: self._map[key] = elems except IOError, err: die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) ) def get_values( self, key ): if key in self._map: rval = self._map[key] if len( rval ) == 1: return rval[0] else: return rval else: die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) ) def get_values_if_exists( self, key ): if key in self._map: rval = self._map[key] if len( rval ) == 1: return rval[0] else: return rval else: return None