BLAST+ new arguments -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids etc

[jandrovins]

Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

import sys; print(sys.version)
3.6.2 |Continuum Analytics, Inc.| (default, Jul 20 2017, 13:51:32) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

import platform; print(platform.python_implementation()); print(platform.platform())
CPython
Linux-2.6.32-504.16.2.el6.x86_64-x86_64-with-centos-6.6-Final

import Bio; print(Bio.__version__)
1.75.dev0

Expected behaviour

Run python setup.py test and test_NCBI_BLAST_tools to be ok without verbosity,

Actual behaviour

Run python setup.py test and in test_NCBI_BLAST_tools:

test_NCBI_BLAST_tools ... /home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ blastp and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ blastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: 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: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ makeblastdb and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -blastdb_version)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: 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: -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ rpsblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -sorthits,-sorthsps,-subject_besthit)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: 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: -sorthits,-sorthsps)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ tblastn and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
/home/vaarcilal/SANDBOX/BIOPYTHON/biopython/Tests/test_NCBI_BLAST_tools.py:403: UserWarning: NCBI BLAST+ tblastx and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
  ",".join(sorted(missing))))
ok

Steps to reproduce

Clone the repository

python setup.py build
python setup.py install
python setup.py test

[nimne]

What version of NCBI BLAST+ is installed? You can find this out by running blastn -version (or any of the other BLAST+ commands).

[jandrovins]

blastn: 2.9.0+

[peterjc]

It looks like the NCBI have added several new arguments to the command line tools: -negative_taxidlist, -negative_taxids, -sorthits, -sorthsps, -subject_besthit, -taxidlist, -taxids (etc).

We need to update file Bio/Blast/Applications.py (harder) and then tweak Tests/test_NCBI_BLAST_tools.py so it won't complain on older versions of BLAST (easy).

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

https://github.com/biopython/biopython/blob/biopython-174/Tests/test_NCBI_BLAST_tools.py#L268

@jandrovins - Thank you for reporting the issue. Is this something you would like to try adding?

[jandrovins]

Yes, I can give it a try! This week will be very busy for me, this would be ready in about 10 days if I take too long.

Would this be OK?

[peterjc]

That'd be fine - thank you 👍

To avoid code duplication, you'll need to work out which of the new commands are shared between tools, and hopefully they will match one of the classes which the individual command wrappers subclass. Please ask if you get stuck, or if we need to explain anything in more detail.

[peterjc]

See also #2863

[peterjc]

See also #2877, we are leaning towards deprecating the Bio.Application framework.

[nick-youngblut]

Given that this issue is still open, and https://github.com/biopython/biopython/blob/master/Bio/Blast/Applications.py doesn't include -negative_taxids, I'm going to assume that this feature has not yet been added, correct? @jandrovins are you still planning on adding the new options?

[peterjc]

I'm personally not planning to add these arguments to the BLAST+ wrappers, and discussions on #2877 have progressed to pull request #3344 deprecating the wrapper framework. Now would be a good time to speak up if you would rather we keep the wrappers, otherwise I am inclined to include this deprecation in the next release (likely later this month).

[peterjc]

Closing as won't fix - we're deprecating the wrappers instead. See also #3471 for updating the examples in the Tutorial.