Source Code for Module bpm.bpmreader

 1  ''' 
 2  Provides a function to read and parse a BPM file into a nice data structure. 
 3  ''' 
 4  import csv 
 5  import os 
 6  import sys 
 7   
 8 -def read(f): 
 9      ''' 
10      A BPM file reader function. Assumes 'f' is in the CSV file format that is 
11      the output from the 'mkbpms' program. (i.e., one module per line with the  
12      module name in the first column followed by its genes in subsequent  
13      columns.) 
14   
15      The returned data structure is a list of tuples. Each tuple represents a 
16      BPM where the first element is a list of genes in the first module and 
17      the second element is a list of genes in the second module. 
18   
19      i.e., [([Gene], [Gene])] 
20      ''' 
21      if not os.access(f, os.R_OK): 
22          print >> sys.stderr, 'Cannot read %s' % f 
23          sys.exit(1) 
24   
25      bpms = [] # a list of two-tuples 
26   
27      reader = csv.reader(open(f), delimiter='\t') 
28      for mod1 in reader: 
29          mod2 = reader.next()  
30          bpms.append((mod1[1:], mod2[1:])) 
31   
32      return bpms 
33