Merge pull request #9 from zhaoc1/master

python3

README.md

@@ -4,3 +4,4 @@ DNAbc
 Identify DNA barcodes in high-throughput sequencing data files and write
 demultiplexed data in a variety of formats.
 
+Build on python3.5

dnabclib/assigner.py

@@ -2,11 +2,11 @@
 
 
 class BarcodeAssigner(object):
-    def __init__(self, samples, mismatches=1, revcomp=True):
+    def __init__(self, samples, mismatches=0, revcomp=True):
         self.samples = samples
-        if mismatches not in [0, 1, 2]:
+        if mismatches not in [0]:
             raise ValueError(
-                "Only 0, 1, or 2 mismatches allowed (got %s)" % mismatches)
+                "Only 0 mismatches allowed (got %s)" % mismatches)
         self.mismatches = mismatches
         self.revcomp = revcomp
         # Sample names assumed to be unique after validating input data

dnabclib/main.py

@@ -89,9 +89,9 @@ def main(argv=None):
     samples = list(Sample.load(args.barcode_file))
 
     writer_cls = writers[config["output_format"]]
-    if os.path.exists(args.output_dir):
-        p.error("Output directory already exists")
-    os.mkdir(args.output_dir)
+    if not os.path.exists(args.output_dir):
+       #p.error("Output directory already exists")
+       os.mkdir(args.output_dir)
     writer = writer_cls(args.output_dir)
 
     if args.index_reads is None:

dnabclib/seqfile.py

@@ -15,7 +15,7 @@ def demultiplex(self, assigner, writer):
         idxs = (FastqRead(x) for x in parse_fastq(self.index_file))
         fwds = (FastqRead(x) for x in parse_fastq(self.forward_file))
         revs = (FastqRead(x) for x in parse_fastq(self.reverse_file))
-        for idx, fwd, rev in itertools.izip(idxs, fwds, revs):
+        for idx, fwd, rev in zip(idxs, fwds, revs):
             sample = assigner.assign(idx.seq)
             writer.write((fwd, rev), sample)
         return assigner.read_counts
@@ -34,7 +34,7 @@ def __init__(self, fwd, rev):
     def demultiplex(self, assigner, writer):
         fwds = (FastqRead(x) for x in parse_fastq(self.forward_file))
         revs = (FastqRead(x) for x in parse_fastq(self.reverse_file))
-        for fwd, rev in itertools.izip(fwds, revs):
+        for fwd, rev in zip(fwds, revs):
             barcode_seq = self._parse_barcode(fwd.desc)
             sample = assigner.assign(barcode_seq)
             writer.write((fwd, rev), sample)
@@ -67,7 +67,7 @@ def _grouper(iterable, n):
     "Collect data into fixed-length chunks or blocks"
     # grouper('ABCDEFG', 3) --> ABC DEF
     args = [iter(iterable)] * n
-    return itertools.izip(*args)
+    return zip(*args)
 
 
 def parse_fastq(f):

dnabclib/writer.py

@@ -7,8 +7,8 @@ def _get_sample_fp(self, sample):
 
 
 def _get_sample_paired_fp(self, sample):
-    fn1 = "PCMP_%s_R1%s" % (sample.name, self.ext)
-    fn2 = "PCMP_%s_R2%s" % (sample.name, self.ext)
+    fn1 = "%s_R1%s" % (sample.name, self.ext)
+    fn2 = "%s_R2%s" % (sample.name, self.ext)
     return (
         os.path.join(self.output_dir, fn1),
         os.path.join(self.output_dir, fn2))

test/test_assigner.py

@@ -1,5 +1,5 @@
 from collections import namedtuple
-from cStringIO import StringIO
+from io import StringIO
 import os
 import shutil
 import tempfile

test/test_main.py

@@ -85,8 +85,8 @@ class SampleNameTests(unittest.TestCase):
     def test_get_sample_names_main(self):
         barcode_file = tempfile.NamedTemporaryFile()
         barcode_file.write(
-            "SampleA\tAAGGAAGG\n"
-            "SampleB\tACGTACGT\n")
+            b"SampleA\tAAGGAAGG\n"
+            b"SampleB\tACGTACGT\n")
         barcode_file.seek(0)
 
         output_file = tempfile.NamedTemporaryFile()
@@ -99,7 +99,7 @@ def test_get_sample_names_main(self):
         output_file.seek(0)
         observed_sample_names = output_file.read()
 
-        self.assertEqual(observed_sample_names, "SampleA\nSampleB\n")
+        self.assertEqual(observed_sample_names, b"SampleA\nSampleB\n")
 
 if __name__ == "__main__":
     unittest.main()

test/test_seqfile.py

@@ -1,5 +1,5 @@
 import collections
-from cStringIO import StringIO
+from io import StringIO
 import os.path
 import shutil
 import tempfile
@@ -21,7 +21,6 @@ def write(self, x, sample):
         else:
             self.written[sample.name].append(x)
 
-
 MockSample = collections.namedtuple("MockSample", "name barcode")
 
 

test/test_writer.py

@@ -25,7 +25,8 @@ def test_write(self):
         w.close()
 
         fp = w._get_output_fp(s1)
-        obs_output = open(fp).read()
+        with open(fp) as f:
+        	obs_output = f.read()
         self.assertEqual(obs_output, ">Read0\nACCTTGG\n")
 
         self.assertFalse(os.path.exists(w._get_output_fp(s2)))
@@ -49,7 +50,8 @@ def test_write(self):
         w.close()
 
         fp = w._get_output_fp(s1)
-        obs_output = open(fp).read()
+        with open(fp) as f:
+        	obs_output = f.read()
 
         self.assertEqual(obs_output, "@Read0\nACCTTGG\n+\n#######\n")
 
@@ -79,10 +81,12 @@ def test_write(self):
 
         fp1, fp2 = w._get_output_fp(s1)
 
-        obs1 = open(fp1).read()
+        with open(fp1) as f:
+        	obs1 = f.read()
         self.assertEqual(obs1, "@Read0\nACCTTGG\n+\n#######\n")
 
-        obs2 = open(fp2).read()
+        with open(fp2) as f:
+        	obs2 = f.read()
         self.assertEqual(obs2, "@Read1\nGCTAGCT\n+\n;342dfA\n")
 
         self.assertFalse(any(