Re: Adding python3-biopython
Hi Peter,
I can confirm that I'm working on the python3 packages. I'm not
finished yet but I included more verbose testing into the packaging and
when I did so I realised some incompatibilities with bwa:
ERROR: test_sampe (test_BWA_tool.BwaTestCase)
Test for generating samfile by paired end sequencing
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BWA_tool.py", line 113, in test_sampe
self.do_aln(self.infile1, self.saifile1)
File "test_BWA_tool.py", line 90, in do_aln
stdout, stderr = cmdline(stdout=out_file)
File "/tmp/buildd/python-biopython-1.63/Bio/Application/__init__.py", line 511, in __call__
stdout_str, stderr_str)
ApplicationError: Command 'bwa aln /tmp/buildd/python-biopython-1.63/Tests/BWA/human_g1k_v37_truncated.fasta /tmp/buildd/python-biopython-1.63/Tests/BWA/HNSCC1_1_truncated.fastq' returne
======================================================================
ERROR: test_samse (test_BWA_tool.BwaTestCase)
Test for single end sequencing
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_BWA_tool.py", line 102, in test_samse
stdout, stderr = cmdline(stdout=self.samfile1)
File "/tmp/buildd/python-biopython-1.63/Bio/Application/__init__.py", line 511, in __call__
stdout_str, stderr_str)
ApplicationError: Command 'bwa samse /tmp/buildd/python-biopython-1.63/Tests/BWA/human_g1k_v37_truncated.fasta /tmp/buildd/python-biopython-1.63/Tests/BWA/1.sai /tmp/buildd/python-biopyt
The used bwa says:
$ bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.6a-r433
Contact: Heng Li <lh3@sanger.ac.uk>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
Note: To use BWA, you need to first index the genome with `bwa index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
first. Please `man ./bwa.1' for the manual.
I think you should adjust your test somehow to make sure that
also the latest bwa version will succeed.
Kind regards
Andreas.
On Mon, Mar 03, 2014 at 02:08:52PM +0000, Peter Cock wrote:
> Hello Philipp & DebianMed,
>
> The last few releases of Biopython supported Python 3
> via 2to3, but as of Biopython 1.63 (released December
> 2013) we have a single codebase which works on both
> Python 2.6/2.7 and Python 3.3+.
...
--
http://fam-tille.de
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