Getting ready for release.

.travis.yml

@@ -7,6 +7,7 @@ python:
 - '2.6'
 - pypy
 install:
+- pip install biopython
 - pip install -e .
 script: nosetests
 deploy:

README.rst

@@ -215,6 +215,16 @@ CLI Usage
 Changes
 -------
 
+*New in version 0.2.5*:
+
+- Fasta and Faidx can take `default_seq` in addition to `as_raw`, `key_function`,
+  and `strict_bounds` parameters.
+- Fixed issue [#20](https://github.com/mdshw5/pyfaidx/issues/20)
+- Faidx has attribute `raw_index` which is a list representing the fai file.
+- Faidx has `rebuild_index` and `write_fai` functions for building and writing
+  `raw_index` to file.
+- Extra test cases, and test cases against Biopython SeqIO
+
 *New in version 0.2.4*:
 
 - Faidx index order is stable and non-random

setup.py

@@ -9,7 +9,7 @@
 setup(
     name='pyfaidx',
     provides='pyfaidx',
-    version='0.2.4',
+    version='0.2.5',
     author='Matthew Shirley',
     author_email='[email protected]',
     url='http://mattshirley.com',

tests/test_bio_seqio.py

@@ -0,0 +1,23 @@
+import os
+from pyfaidx import Fasta, FetchError
+from Bio import SeqIO
+
+path = os.path.dirname(__file__)
+os.chdir(path)
+
+class TestBioSeqIO:
+    def __init__(self):
+        self.genes = os.path.join(path, 'data/genes.fasta')
+        self.fasta = Fasta(self.genes)
+        with open(self.genes, "rU") as fh:
+            self.seqio = SeqIO.to_dict(SeqIO.parse(fh, "fasta"))
+
+    def test_fetch_whole_entry(self):
+        assert str(self.fasta['KF435150.1']) == str(self.seqio['KF435150.1'].seq)
+        assert self.fasta['KF435150.1'].name == str(self.seqio['KF435150.1'].name)
+
+    def test_slice_whole_entry(self):
+        assert str(self.fasta['KF435150.1'][::3]) == str(self.seqio['KF435150.1'].seq[::3])
+
+    def test_revcomp_whole_entry(self):
+        assert str(self.fasta['KF435150.1'][:].reverse.complement) == str(self.seqio['KF435150.1'].reverse_complement().seq)