You are viewing a plain text version of this content. The canonical link for it is here.
Posted to issues@beam.apache.org by "Valentyn Tymofieiev (Jira)" <ji...@apache.org> on 2021/06/09 01:10:00 UTC
[jira] [Commented] (BEAM-5628) VcfIO is not Python3-compatible and
there are no plans to make it compatible.
[ https://issues.apache.org/jira/browse/BEAM-5628?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17359679#comment-17359679 ]
Valentyn Tymofieiev commented on BEAM-5628:
-------------------------------------------
VCF IO has been cleaned away as discussed in https://lists.apache.org/thread.html/rfca8b756aaeaf57069ed6f5b3026f94b1a7e11bbd6b212d36fdce5e2%40%3Cdev.beam.apache.org%3E.
The last Beam SDK that supports VCF IO on Python 2 is 2.24.0.
> VcfIO is not Python3-compatible and there are no plans to make it compatible.
> -----------------------------------------------------------------------------
>
> Key: BEAM-5628
> URL: https://issues.apache.org/jira/browse/BEAM-5628
> Project: Beam
> Issue Type: Sub-task
> Components: sdk-py-core
> Reporter: Valentyn Tymofieiev
> Priority: P3
> Time Spent: 3h 10m
> Remaining Estimate: 0h
>
> Several VcfIO tests fail in Python 3 with TypeError: cannot use a string pattern on a bytes-like object
>
> ERROR: test_read_after_splitting (apache_beam.io.vcfio_test.VcfSourceTest)
> "
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/vcfio_test.py"", line 336, in test_read_after_splitting
> ] split_records.extend(source_test_utils.read_from_source(*source_info))
> ] File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/source_test_utils.py"", line 101, in read_from_source
> for value in reader:
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/vcfio.py"", line 264, in read_records
> for line in record_iterator:
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/vcfio.py"", line 330, in __next__
> record = next(self._vcf_reader)
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/target/.tox/py3/lib/python3.5/site-packages/vcf/parser.py"", line 543, in __next__
> row = self._row_pattern.split(line.rstrip())
> TypeError: cannot use a string pattern on a bytes-like object
> "
--
This message was sent by Atlassian Jira
(v8.3.4#803005)