diff LocationFile.py @ 14:8ae67e9fb6ff

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
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line diff
--- /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