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Python 3.2 compatibility tweaks #59

Merged
merged 2 commits into from

2 participants

@msabramo
~/dev/git-repos/PyVCF$ tox
...
  py26: commands succeeded
  py27: commands succeeded
  py32: commands succeeded
  congratulations :)

Note that there's no released pysam that supports Python 3 yet so I ended up skipping fetch in the doctests.

@jamescasbon jamescasbon merged commit c09858f into jamescasbon:master
@jamescasbon
Owner

Thanks!

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Showing with 14 additions and 12 deletions.
  1. +3 −1 tox.ini
  2. +10 −10 vcf/__init__.py
  3. +1 −1 vcf/test/test_vcf.py
View
4 tox.ini
@@ -7,7 +7,9 @@
envlist = py26, py27, py32
[testenv]
-commands = python setup.py test
+commands =
+ rm -rf {toxinidir}/build
+ python setup.py test
[testenv:py26]
deps =
View
20 vcf/__init__.py
@@ -15,7 +15,7 @@
object and acts as a reader::
>>> import vcf
- >>> vcf_reader = vcf.Reader(open('vcf/test/example-4.0.vcf', 'rb'))
+ >>> vcf_reader = vcf.Reader(open('vcf/test/example-4.0.vcf', 'r'))
>>> for record in vcf_reader:
... print record
Record(CHROM=20, POS=14370, REF=G, ALT=[A])
@@ -50,7 +50,7 @@
of key=value pairs are converted to Python dictionaries, with flags being given
a ``True`` value. Integers and floats are handled exactly as you'd expect::
- >>> vcf_reader = vcf.Reader(open('vcf/test/example-4.0.vcf', 'rb'))
+ >>> vcf_reader = vcf.Reader(open('vcf/test/example-4.0.vcf', 'r'))
>>> record = vcf_reader.next()
>>> print record.POS
14370
@@ -135,7 +135,7 @@
ALT records are actually classes, so that you can interrogate them::
- >>> reader = vcf.Reader(file('vcf/test/example-4.1-bnd.vcf'))
+ >>> reader = vcf.Reader(open('vcf/test/example-4.1-bnd.vcf'))
>>> _ = reader.next(); row = reader.next()
>>> print row
Record(CHROM=1, POS=2, REF=T, ALT=[T[2:3[])
@@ -147,14 +147,14 @@
region you are interested in::
>>> vcf_reader = vcf.Reader(filename='vcf/test/tb.vcf.gz')
- >>> for record in vcf_reader.fetch('20', 1110696, 1230237):
+ >>> for record in vcf_reader.fetch('20', 1110696, 1230237): # doctest: +SKIP
... print record
Record(CHROM=20, POS=1110696, REF=A, ALT=[G, T])
Record(CHROM=20, POS=1230237, REF=T, ALT=[None])
Or extract a single row::
- >>> print vcf_reader.fetch('20', 1110696)
+ >>> print vcf_reader.fetch('20', 1110696) # doctest: +SKIP
Record(CHROM=20, POS=1110696, REF=A, ALT=[G, T])
@@ -162,7 +162,7 @@
template ``Reader`` which provides the metadata::
>>> vcf_reader = vcf.Reader(filename='vcf/test/tb.vcf.gz')
- >>> vcf_writer = vcf.Writer(file('/dev/null', 'w'), vcf_reader)
+ >>> vcf_writer = vcf.Writer(open('/dev/null', 'w'), vcf_reader)
>>> for record in vcf_reader:
... vcf_writer.write_record(record)
@@ -172,9 +172,9 @@
see :doc:`FILTERS` for full description.
'''
-from parser import Reader, Writer
-from parser import VCFReader, VCFWriter
-from filters import Base as Filter
-from parser import RESERVED_INFO, RESERVED_FORMAT
+from vcf.parser import Reader, Writer
+from vcf.parser import VCFReader, VCFWriter
+from vcf.filters import Base as Filter
+from vcf.parser import RESERVED_INFO, RESERVED_FORMAT
VERSION = '0.5.0-pre'
View
2 vcf/test/test_vcf.py
@@ -198,7 +198,7 @@ def testParse(self):
def test_issue_49(self):
"""docstring for test_issue_49"""
- reader = vcf.Reader(fh('issue_49.vcf', 'rb'))
+ reader = vcf.Reader(fh('issue_49.vcf', 'r'))
self.assertEqual(len(reader.samples), 0)
for _ in reader:
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