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

[Fulton, Ben]

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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