[Biopython-dev] Fwd: [blast-announce] A new version (2.6.0) of the BLAST+ executable is available.

Fri Jan 27 14:40:07 UTC 2017

I apologize; I ran the tests against an older version. The only new options
available in 2.6 are for rpstblastn: -comp_based_stats and -use_sw_tback .
I've submitted a pull request for those.

IMO the blast command lines would be better expressed as composition rather
than inheritance. Any objection to me spending some time on that after the 
1.69 release?

--
Ben Fulton
Research Technologies
Scientific Applications and Performance Tuning
Indiana University
E-Mail: befulton at iu.edu

-----Original Message-----
From: Fulton, Ben
Sent: Tuesday, January 24, 2017 11:20 PM
To: 'Peter Cock' <p.j.a.cock at googlemail.com>
Cc: Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
Subject: RE: [Biopython-dev] Fwd: [blast-announce] A new version (2.6.0) of
the BLAST+ executable is available.

Hmm. I'll take a look at it; but the parameters that are missing are exactly
the ones that are mentioned in the commit to which you linked. Maybe they've
been dropped again somewhere.

--
Ben Fulton
Research Technologies
Scientific Applications and Performance Tuning
Indiana University
E-Mail: befulton at iu.edu

-----Original Message-----
From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
Sent: Thursday, January 19, 2017 9:13 AM
To: Fulton, Ben <befulton at iu.edu>
Cc: Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
Subject: Re: [Biopython-dev] Fwd: [blast-announce] A new version (2.6.0) of
the BLAST+ executable is available.

Thanks Ben,

That looks like relatively few new parameters have been added:

deltablast -save_each_pssm -save_pssm_after_last_round

psiblast -save_each_pssm -save_pssm_after_last_round

rpstblastn -comp_based_stats -use_sw_tback

This means additions to the wrappers' parameter lists (and/or
moving parameters to base classes now more tools use them):

https://github.com/biopython/biopython/blob/master/Bio/Blast/Applications.py

And, a minor tweak to the test script. As an example, a
recent change of this kind was:

https://github.com/biopython/biopython/commit/abde2348cbe5f1aa73466232c17b746fb9a8ee6a

If you're happy to tackle this, I would welcome a pull request.

Regards,

Peter

On Thu, Jan 19, 2017 at 1:07 AM, Fulton, Ben <befulton at iu.edu> wrote:
> Here are the results of running the tests against Python 3.5 on Windows:
>
> C:\Apps\Python3.5-32\python.exe
> C:/Users/befulton/Documents/GIT/biopython/Tests/test_NCBI_BLAST_tools.py
> test_blastn (__main__.CheckCompleteArgList)
> Check all blastn arguments are supported ... ok
> test_blastp (__main__.CheckCompleteArgList)
> Check all blastp arguments are supported ... ok
> test_blastx (__main__.CheckCompleteArgList)
> Check all blastx arguments are supported ... ok
> test_deltablast (__main__.CheckCompleteArgList)
> Check all deltablast arguments are supported ...
> C:/Users/befulton/Documents/GIT/biopython/Tests/test_NCBI_BLAST_tools.py:280
> : UserWarning: NCBI BLAST+ deltablast and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing: -save_each_pssm,-save_pssm_after_last_round)
>   ",".join(sorted(missing))))
> ok
> test_psiblast (__main__.CheckCompleteArgList)
> Check all psiblast arguments are supported ...
> C:/Users/befulton/Documents/GIT/biopython/Tests/test_NCBI_BLAST_tools.py:280
> : UserWarning: NCBI BLAST+ psiblast and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing: -save_each_pssm,-save_pssm_after_last_round)
>   ",".join(sorted(missing))))
> ok
> test_rpsblast (__main__.CheckCompleteArgList)
> Check all rpsblast arguments are supported ... ok
> test_rpstblastn (__main__.CheckCompleteArgList)
> Check all rpstblastn arguments are supported ...
> C:/Users/befulton/Documents/GIT/biopython/Tests/test_NCBI_BLAST_tools.py:280
> : UserWarning: NCBI BLAST+ rpstblastn and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing: -comp_based_stats,-use_sw_tback)
>   ",".join(sorted(missing))))
> ok
> test_tblastn (__main__.CheckCompleteArgList)
> Check all tblastn arguments are supported ... ok
> test_tblastx (__main__.CheckCompleteArgList)
> Check all tblastx arguments are supported ... ok
> test_blastn (__main__.Pairwise)
> Pairwise BLASTN search ... ok
> test_blastp (__main__.Pairwise)
> Pairwise BLASTP search ... FAIL
> test_tblastn (__main__.Pairwise)
> Pairwise TBLASTN search ... ok
>
> ======================================================================
> FAIL: test_blastp (__main__.Pairwise)
> Pairwise BLASTP search
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "C:/Users/befulton/Documents/GIT/biopython/Tests/test_NCBI_BLAST_tools.py",
> line 103, in test_blastp
>     self.assertEqual(10, stdoutdata.count("Query= "))
> AssertionError: 10 != 1
>
> ----------------------------------------------------------------------
> Ran 12 tests in 0.485s
>
> FAILED (failures=1)
>
> Process finished with exit code 1
>
> --
> Ben Fulton
> Research Technologies
> Scientific Applications and Performance Tuning
> Indiana University
> E-Mail: befulton at iu.edu
>
>
> -----Original Message-----
> From: Biopython-dev
> [mailto:biopython-dev-bounces+befulton=iu.edu at mailman.open-bio.org] On
> Behalf Of Peter Cock
> Sent: Saturday, January 14, 2017 2:28 PM
> To: Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
> Subject: [Biopython-dev] Fwd: [blast-announce] A new version (2.6.0) of the
> BLAST+ executable is available.
>
> If someone would like to check if our BLAST+ command
> line wrappers need updating, that would be great.
>
> Just running test_NCBI_BLAST_tools.py should say if
> any tools have added/removed command line switches.
>
> Peter
>
> ---------- Forwarded message ----------
> From: Mcginnis, Scott (NIH/NLM/NCBI) [E] <mcginnis at ncbi.nlm.nih.gov>
> Date: Thu, Jan 12, 2017 at 6:07 PM
> Subject: [blast-announce] A new version (2.6.0) of the BLAST+
> executable is available.
> To: NLM/NCBI List blast-announce <blast-announce at ncbi.nlm.nih.gov>
>
>
>
>
> A new version (2.6.0) of the BLAST+ executable is available.
>
> This new version offers improved support for use of accession.version
> as the primary NCBI identifier. The speed of blastdbcmd when dumping
> information from a database (e.g., all GIs or all accessions) has been
> improved. A number of other bug fixes and improvements are also
> included. Future releases will continue to improve the support for
> accession.version as the main NCBI identifier.
>
> The release notes are at http://www.ncbi.nlm.nih.gov/books/NBK131777/
>
> The new executables are available on the NCBI FTP site at
> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
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