[Biopython-dev] BWA command line change?

[Saket Choudhary]

This is turning out to be an issue with this particular version of
bwa[0.7.6a-r433];l
$ bwa7.6a aln
[main] unrecognized command 'aln'

However the later two versions do support it, and the tests do pass:


$ bwa7.8 aln

Usage:   bwa aln [options] <prefix> <in.fq>

$ bwa7.7 aln

Usage:   bwa aln [options] <prefix> <in.fq>


I have bwa7.5[ 0.7.5a-r405] installed which I used for testing and it
seems to be working as well.

Unfortunately, I was not able to locate this error being reported on
the bwa mailing list[The reason probably being more people using 'mem'
now]

Andrew, can you check this with the latest version of bwa?[0.7.8]

Thanks,
Saket


On 27 April 2014 18:13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi Saket,
>
> Could you have a look at this BWA problem Andreas found
> while testing the Debian package?
>
> I have just reordered the error message in Bio.Application
> to put the return code earlier in case the exception text is
> truncated (as here):
> https://github.com/biopython/biopython/commit/9860973c05aeb102f82e217ff3a88e241a3ba620
>
> I've also switched to relative paths which will also shorten
> the error message:
> https://github.com/biopython/biopython/commit/a03d23760783c157ff7c30f483ace55beda31c09
>
> I just tested with BWA 0.6.1 (in the Debian repository on
> my old desktop), and test_BWA_tool.py was fine.
>
> Thanks,
>
> Peter
>
>
> ---------- Forwarded message ----------
> From: Andreas Tille <andreas at an3as.eu>
> Date: Tue, Mar 4, 2014 at 8:18 PM
> Subject: Re: Adding python3-biopython
> To: Peter Cock <p.j.a.cock at googlemail.com>
> Cc: Debian Med Project List <debian-med at lists.debian.org>, Philipp
> Benner <philipp at debian.org>
>
>
> 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 at 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