Move region splitting functions to pyfaidx module.

README.rst

@@ -218,6 +218,10 @@ A lower-level Faidx class is also available:
 Changes
 -------
 
+*New in version 0.2.8*:
+
+- Small internal refactoring
+
 *New in version 0.2.7*:
 
 - Faidx and Fasta `strict_bounds` bounds checking logic is more correct

pyfaidx/__init__.py

@@ -455,6 +455,30 @@ def map_to_function(rname):
     return map_to_function
 
 
+def bed_split(bed_entry):
+    try:
+        rname, start, end = bed_entry.rstrip().split()[:3]
+    except IndexError:
+        raise BedError('Malformed BED entry! {0}\n'.format(bed_entry.rstrip()))
+    start, end = (int(start), int(end))
+    return (rname, start, end)
+
+
+def ucsc_split(region):
+    region = region.split()[0]
+    try:
+        rname, interval = region.split(':')
+    except ValueError:
+        rname = region
+        interval = None
+    try:
+        start, end = interval.split('-')
+        start, end = (int(start) - 1, int(end))
+    except (AttributeError, ValueError):
+        start, end = (None, None)
+    return (rname, start, end)
+
+
 if __name__ == "__main__":
     import doctest
     doctest.testmod()

pyfaidx/cli.py

@@ -20,7 +20,7 @@
 
 import argparse
 import sys
-from pyfaidx import Fasta, wrap_sequence, FetchError, BedError, RegionError
+from pyfaidx import Fasta, wrap_sequence, FetchError, BedError, RegionError, ucsc_split, bed_split
 
 
 def write_sequence(args):
@@ -41,30 +41,6 @@ def write_sequence(args):
     fasta.__exit__()
 
 
-def bed_split(bed_entry):
-    try:
-        rname, start, end = bed_entry.rstrip().split()[:3]
-    except IndexError:
-        raise BedError('Malformed BED entry! {0}\n'.format(bed_entry.rstrip()))
-    start, end = (int(start), int(end))
-    return (rname, start, end)
-
-
-def ucsc_split(region):
-    region = region.split()[0]
-    try:
-        rname, interval = region.split(':')
-    except ValueError:
-        rname = region
-        interval = None
-    try:
-        start, end = interval.split('-')
-        start, end = (int(start) - 1, int(end))
-    except (AttributeError, ValueError):
-        start, end = (None, None)
-    return (rname, start, end)
-
-
 def fetch_sequence(args, fasta, rname, start=None, end=None):
     line_len = fasta.faidx.index[rname].lenc
     sequence = fasta[rname][start:end]

setup.py

@@ -9,7 +9,7 @@
 setup(
     name='pyfaidx',
     provides='pyfaidx',
-    version='0.2.7',
+    version='0.2.8',
     author='Matthew Shirley',
     author_email='[email protected]',
     url='http://mattshirley.com',