Merge pull request #31 from mdshw5/FastaRecord.__iter__

Closes #31. Closes #32.

.travis.yml

@@ -2,11 +2,13 @@ language: python
 python:
 - '3.4'
 - '3.3'
+- '3.2'
 - '2.7'
 - '2.6'
 - pypy
+- pypy3
 install:
-- pip install biopython
+- pip install biopython || true
 - pip install -e .
 script: nosetests
 deploy:

pyfaidx/__init__.py

@@ -391,6 +391,7 @@ class FastaRecord(object):
     def __init__(self, name, fa):
         self.name = name
         self._fa = fa
+        self._len = self._fa.faidx.index[self.name].rlen
 
     def __getitem__(self, n):
         """Return sequence from region [start, end)
@@ -416,12 +417,23 @@ def __getitem__(self, n):
         except FetchError:
             raise
 
+    def __iter__(self):
+        line_len = self._fa.faidx.index[self.name].lenc
+        start = 0
+        while True:
+            end = start + line_len
+            if end < len(self):
+                yield self[start:end]
+            else:
+                yield self[start:]
+                raise StopIteration
+            start += line_len
+
     def __repr__(self):
         return 'FastaRecord("%s")' % (self.name)
 
     def __len__(self):
-        """ Return length of chromosome """
-        return self._fa.faidx.index[self.name].rlen
+        return self._len
 
     def __str__(self):
         return str(self[:])

tests/test_FastaRecord_iter.py

@@ -0,0 +1,19 @@
+import os
+from pyfaidx import Fasta
+
+path = os.path.dirname(__file__)
+os.chdir(path)
+
+class TestFastaRecordIter:
+    def __init__(self):
+        self.genes = os.path.join(path, 'data/genes.fasta')
+        self.fasta = Fasta(self.genes)
+
+    def test_fetch_whole_fasta(self):
+        expect = open(self.genes).read()
+        result = ''.join(['>' + record.name + '\n' + ''.join([line.seq + '\n' for line in record]) for record in self.fasta]).rstrip()
+        assert expect == result
+
+    def test_line_len(self):
+        for record in self.fasta:
+            assert len(next(iter(record))) == self.fasta.faidx.index[record.name].lenc

tests/test_bio_seqio.py

@@ -1,6 +1,11 @@
 import os
 from pyfaidx import Fasta, FetchError
-from Bio import SeqIO
+from nose.plugins.skip import Skip, SkipTest
+try:
+    from Bio import SeqIO
+    test_bio = True
+except ImportError:
+    test_bio = False
 
 path = os.path.dirname(__file__)
 os.chdir(path)
@@ -9,15 +14,25 @@ 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"))
+        if test_bio:
+            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)
+        if test_bio:
+            assert str(self.fasta['KF435150.1']) == str(self.seqio['KF435150.1'].seq)
+            assert self.fasta['KF435150.1'].name == str(self.seqio['KF435150.1'].name)
+        else:
+            raise SkipTest
 
     def test_slice_whole_entry(self):
-        assert str(self.fasta['KF435150.1'][::3]) == str(self.seqio['KF435150.1'].seq[::3])
+        if test_bio:
+            assert str(self.fasta['KF435150.1'][::3]) == str(self.seqio['KF435150.1'].seq[::3])
+        else:
+            raise SkipTest
 
     def test_revcomp_whole_entry(self):
-        assert str(self.fasta['KF435150.1'][:].reverse.complement) == str(self.seqio['KF435150.1'].reverse_complement().seq)
+        if test_bio:
+            assert str(self.fasta['KF435150.1'][:].reverse.complement) == str(self.seqio['KF435150.1'].reverse_complement().seq)
+        else:
+            raise SkipTest