Mercurial > repos > miller-lab > genome_diversity

comparison LocationFile.py @ 14:8ae67e9fb6ff

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Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
author miller-lab
date Fri, 28 Sep 2012 11:35:56 -0400
parents 4b6590dd7250
children
comparison
equal deleted inserted replaced
13:fdb4240fb565 14:8ae67e9fb6ff
1 #!/usr/bin/env python
2
3 import sys
4
5 def die( message ):
6 print >> sys.stderr, message
7 sys.exit(1)
8
9 def open_or_die( filename, mode='r', message=None ):
10 if message is None:
11 message = 'Error opening {0}'.format( filename )
12 try:
13 fh = open( filename, mode )
14 except IOError, err:
15 die( '{0}: {1}'.format( message, err.strerror ) )
16 return fh
17
18 class LocationFile( object ):
19 def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ):
20 self.filename = filename
21 if comment_chars is None:
22 self.comment_chars = ( '#' )
23 else:
24 self.comment_chars = tuple( comment_chars )
25 self.delimiter = delimiter
26 self.key_column = key_column
27 self._map = {}
28 self._populate_map()
29
30 def _populate_map( self ):
31 try:
32 with open( self.filename ) as fh:
33 line_number = 0
34 for line in fh:
35 line_number += 1
36 line = line.rstrip( '\r\n' )
37 if not line.startswith( self.comment_chars ):
38 elems = line.split( self.delimiter )
39 if len( elems ) <= self.key_column:
40 die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) )
41 else:
42 key = elems.pop( self.key_column )
43 if key in self._map:
44 if self._map[key] != elems:
45 die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) )
46 else:
47 self._map[key] = elems
48 except IOError, err:
49 die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) )
50
51 def get_values( self, key ):
52 if key in self._map:
53 rval = self._map[key]
54 if len( rval ) == 1:
55 return rval[0]
56 else:
57 return rval
58 else:
59 die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) )
60
61 def get_values_if_exists( self, key ):
62 if key in self._map:
63 rval = self._map[key]
64 if len( rval ) == 1:
65 return rval[0]
66 else:
67 return rval
68 else:
69 return None