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

[Peter Cock]

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
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