Break off common file and fasta operations

common.py

@@ -0,0 +1,19 @@
+from optparse import OptionParser, OptionValueError
+
+def parse_seq(f):
+    """Parse a FASTA sequence from the file 'f', returning its full string"""
+    if not f.readline().startswith(">"):
+        raise Exception("Not a FASTA sequence")
+    lines = []
+    for line in f:
+        if line.startswith(">"):
+            break
+        lines += [line.strip()]
+    return ''.join(lines)
+
+def parser_open_file(option, opt_str, value, parser, mode):
+    try:
+        f = open(value, mode)
+    except IOError, e:
+         raise OptionValueError(str(e))
+    setattr(parser.values, option.dest, f)

readGen.py

@@ -2,7 +2,8 @@
 
 import random
 import sys
-from optparse import OptionParser, OptionValueError
+from optparse import OptionParser
+from common import *
 
 def gen_reads(seq, l, coverage=1):
     num_reads = int((len(seq)/l) * coverage)
@@ -21,24 +22,6 @@ def write_reads(rs, f):
         f.write('\t'.join(str(x) for x in read))
         f.write('\n')
 
-def parse_seq(f):
-    """Parse a FASTA sequence from the file 'f', returning its full string"""
-    if not f.readline().startswith(">"):
-        raise Exception("Not a FASTA sequence")
-    lines = []
-    for line in f:
-        if line.startswith(">"):
-            break
-        lines += [line.strip()]
-    return ''.join(lines)
-
-def parser_open_file(option, opt_str, value, parser, mode):
-    try:
-        f = open(value, mode)
-    except IOError, e:
-         raise OptionValueError(str(e))
-    setattr(parser.values, option.dest, f)
-
 if __name__ == "__main__":
     parser = OptionParser(usage="%prog length [options]")