Mercurial > repos > miller-lab > genome_diversity
diff LocationFile.py @ 14:8ae67e9fb6ff
Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
author | miller-lab |
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date | Fri, 28 Sep 2012 11:35:56 -0400 |
parents | 4b6590dd7250 |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LocationFile.py Fri Sep 28 11:35:56 2012 -0400 @@ -0,0 +1,69 @@ +#!/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