de0bb21fb3
Apply isort (forcing single lines, not sorting by type) via ruff
...
$ ruff check --fix --select=I \
--config=lint.isort.force-single-line=true \
--config=lint.isort.order-by-type=false \
BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py
Using ruff version 0.4.10
2024-06-26 15:31:39 +09:00
e5c9cabf8c
pyupgrade: f-strings (easy cases)
...
Ran this:
$ pyupgrade --py37-plus Bio/*.py Bio/*/*.py Bio/*/*/*.py BioSQL/*.py
$ black Bio/ BioSQL/
Then reverted any changes adding a .format method, spotted with:
$ git diff | grep "^+" | grep -E "(\.format|\+\+\+)"
2021-09-11 12:30:38 +01:00
beb3138162
Declare Bio.Application obsolete
...
See discussion on #2877 .
2021-01-25 09:53:30 +00:00
74d65bd42f
Implement makeblastdb -blastdb_version flag ( #2987 )
...
This patch adds support for the `-blastdb_version` switch of the
`makeblastdb` wrapper of the library.
2020-09-04 17:53:11 +01:00
639a815660
some fixes
2020-06-30 21:11:06 +01:00
a5e960c71a
Fix triple quotes in Bio/Blast/Applications.py
...
Applying black formatting made this more obivous.
See issue #2369 .
Also added missing full stops to the first line of
the dynamically created property's docstrings.
2020-01-23 10:39:56 +00:00
6758d9db00
post-black string concatenation
2020-01-23 10:39:56 +00:00
1ccef934e8
black, version 19.10b, Bio/Blast/Applications.py
2020-01-23 10:39:56 +00:00
0c25556525
Removed print_function and division future imports
2019-12-25 14:41:32 +00:00
6b961bef1a
removed extraneous escape characters from docstrings #2220
2019-11-26 13:27:16 +00:00
045ccc4f82
changes to attributes to make rst compatible
2019-11-26 13:27:16 +00:00
b58c4b613b
Using tool unify to convert Bio/ to use double quotes
...
Using https://github.com/myint/unify for this:
$ unify --quote \" --in-place Bio/*.py Bio/*/*.py Bio/*/*/*.py
$ git checkout Bio/Restriction/Restriction_Dictionary.py
Note excluded automatically generated file
Bio/Restriction/Restriction_Dictionary.py
2019-08-02 14:10:22 +01:00
8677e94d3d
Double backticks for RST markup
...
Avoid using single backticks (other than RST links).
2019-07-16 16:56:39 +01:00
d4631248f7
Quote spaces in local NCBI BLAST+ -outfmt argument ( #2071 )
...
* fix issue #2055 , spaces in BLAST+ -outfmt
* clarify documentation of filename argument
* improve BLAST outfmt docstring
2019-05-20 17:15:43 +01:00
a78d72189c
Dual license Bio/Blast/Applications.py
...
The original author Brad Chapman, named copyright holders, and
contributors recorded in version control have all agreed (except
one, see below).
- Adhemar Zerlotini (@azneto)
https://github.com/biopython/biopython/pull/1412#issue-147372599
- Ben Fulton (@benfulton)
https://github.com/biopython/biopython/issues/898#issuecomment-382072311
- Wibowo Arindrarto (@bow)
https://github.com/biopython/biopython/issues/898#issuecomment-236920576
- Carlos Pena (@carlosp420)
https://github.com/biopython/biopython/issues/898#issuecomment-236925650
- Christian Brueffer (@cbrueffer)
https://github.com/biopython/biopython/issues/898#issuecomment-236922857
- Christophe Faucon (@pfaucon)
https://github.com/biopython/biopython/issues/898#issuecomment-236988474
- Brad Chapman (@chapmanb)
http://mailman.open-bio.org/pipermail/biopython-dev/2013-July/019903.html
- Francesco Gastaldello (@gasta88)
https://github.com/biopython/biopython/pull/1063
- Iddo Friedberg (@idoerg)
https://github.com/biopython/biopython/issues/898#issuecomment-380437378
- Michiel de Hoon (@mdehoon)
https://github.com/biopython/biopython/issues/898#issuecomment-237122630
- @morrme
https://github.com/biopython/biopython/pull/1172#issuecomment-295430028
- Nick Negretti (@nimne)
https://github.com/biopython/biopython/pull/1768#issue-210631196
- Peter Cock (@peterjc)
https://github.com/biopython/biopython/issues/898#issue-167420613
- Phillip Garland (@pgarland)
https://github.com/biopython/biopython/issues/898#issuecomment-241300239
- Sergio Valqui (@svalqui)
https://github.com/biopython/biopython/pull/1749
- Vincent DAvis (@vincentdavis)
https://github.com/biopython/biopython/issues/898#issuecomment-236938752
We have not yet secured permission from Jonathan Taylor to dual
license his contributions, but in this case it was to the 'legacy'
BLAST command line tools, and those wrappers were removed in 2014:
18322edbab6f1b9fc7d6
2018-12-20 10:12:05 +00:00
72b3a779d7
Simplified checker function
2018-09-21 17:44:58 +01:00
c7f61ddc2a
Fixed python2 compatibility, and change in older BLAST+
2018-09-21 17:44:58 +01:00
29e8cd23e8
Add testing code
2018-09-21 17:44:58 +01:00
6d96f63b7e
Added rest of makeblastdb switches and options
2018-09-21 17:44:58 +01:00
73108d6c4a
Minimal working makeblastdb wrapper
2018-09-21 17:44:58 +01:00
253ccf9da3
Adding PRIVATE to docstrings ( #1749 )
...
Add (PRIVATE) to the docstrings identified by the grep command:
$ grep --include '*.py' -rn -A 1 "def _[a-z]" Bio BioSQL | grep '"""' | grep -v "(PRIVATE)"
Closes issue #1466 .
2018-08-17 13:45:13 +01:00
cb80747142
Implement negative_seqidlist in BLAST+ wrappers.
...
New in BLAST+ 2.7.1 (or maybe in 2.7.0)
2018-03-14 12:02:05 +00:00
4a1ca63550
Imperative mood for Pathway, NeuralNetwork and Blast (D401)
...
Squashed commit of pull request #1504 , docstyle changes for #1473 .
2018-01-12 14:39:54 +00:00
183143c940
Convert DOI: and doi: to https://doi.org/ format
...
See https://www.crossref.org/display-guidelines/
2017-11-22 10:31:36 +00:00
ba39e1f768
adding the docstring 'Initialize the class.' to every def __init__ with no docstring
2017-10-19 22:20:04 +01:00
80988e819a
corrections for pydocstyle rule D204
2017-05-07 22:36:29 +01:00
7bfb2903a8
autopep8 --in-place --select E305 Bio/*/*.py
2017-04-20 17:15:31 +01:00
acc94ebccf
new BLAST+ options use_sw_tback and comp_based_stats options
...
Squashed commit of pull request #1050
use_sw_tback and comp_based_stats options are available for rpstblastn in blast 2.6.0
2017-03-03 17:14:46 +00:00
676c04c2f7
PEP8 whitespace in Bio/Blast/Applications.py
...
TODO: Still lots of overly long lines
2016-06-13 16:36:24 +01:00
abde2348cb
Couple of new arguments in NCBI BLAST+ 2.3.0
2016-05-19 15:04:17 +01:00
1119425f45
PEP8 E402 module level imports vs __docformat__ placement
...
This was mostly due to the latest version of the pep8
tool being stricter and wanting the __docformat__ line
after the module level imports.
Rather than moving them all, I removed them - and we'll
switch to using reStructuredText as the default when
converting the docstrings into API HTML pages for the
website.
This commit also includes assorted other PEP8 fixes which
our recommend git pre-commit hook spotted, and I fixed by
hand.
2016-05-10 17:13:46 +01:00
c03a67da12
PEP8 fixes
2015-10-29 11:06:38 +02:00
6d5a859354
BLAST+ 2.2.30 deliberately removed -word_size for RPS-BLAST
...
According to the BLAST developers (by email), the word size
is specified when the domain database is built, and so the
option should never should have been in rpsblast and rpstblastn.
TODO: Remove this from our rpsblast and rpstblastn wrappers.
2014-12-02 14:38:34 +00:00
a6fc44725a
RST markup and PEP8 for Bio.Affy, Bio.Align, Bio.Alphabet, Bio.Blast, etc
...
Also fixed an init bug in Bio.Crystal (would reused dict).
2014-11-11 22:23:34 +09:00
40c016b7f8
Fix epydoc RST warning, 'Lists must be indented'
2014-11-11 17:06:09 +09:00
59acc330b6
Addressed TODO's -use_index -soft_masking (BLAST+ wrappers)
2014-11-11 15:43:25 +09:00
27b2c42a9e
BLAST+ 2.2.30 moved new options to base Class
...
The new options `-line_length`, `-qcov_hsp_perc` and `-sum_stats` are common to
several BLAST tools. So I moved them to the base class.
Also, I added exceptions in `test_NCBI_BLAST_tools.py`.
I tested the changes with BLAST+ version 2.2.28 to 2.2.30.
2014-11-02 18:41:59 +00:00
9e8e1b76be
BLAST+ 2.2.30 added three new options to psiblast
2014-11-01 15:54:31 +00:00
c2b3dbe61a
Added BLAST task options "*-fast"
...
Added to `tblastn', `blastp' and `blastx'. Due to recent release of
BLAST+ 2.2.30.
2014-11-01 14:56:13 +00:00
e43c20017a
PEP8 fixes Alphabet, Application, Blast
2014-10-29 10:27:38 +02:00
b0496b342e
autopep8 E203 - Remove extraneous whitespace (colon related)
...
$ autopep8 -r -i --select E203 ...
Note did not apply changes to e.g. Tests/test_Crystal.py and
Bio/SCOP/Raf.py where colon used for numpy array access, nor
auto-generated files like Bio/SubsMat/MatrixInfo.py
2014-10-27 14:28:03 +00:00
27826abf22
Remove EOF whitespace (PEP8 W391).
2014-10-17 15:40:41 +02:00
f07c1d9cc0
Tweaking property names; avoid unneeded triple quotes; indentation
...
Updated deltablast parameter list indentation to match rest of module.
This may not be strictly PEP8, but it helps for showing the property
docstrings on a single line.
2014-05-26 10:44:58 +01:00
e9598b26ff
Added Deltablast options -domain_inclusion_ethresh, -gap_trigger, -inclusion_ethresh, -num_iterations, -out_ascii_pssm, -out_pssm, -pseudocount, -rpsdb, -show_domain_hits
2014-05-17 13:14:49 +01:00
6f1b9fc7d6
Remove deprecated legacy BLAST wrappers from Bio.BLAST.Applications
2014-03-27 15:13:05 +00:00
a033ecc291
Update doctest, deltablast does not have -ungapped
2014-01-16 14:43:19 +00:00
1f0c9561ea
deltablast does not have -task, -ungapped, -db_hard_mask, -db_soft_mask
...
Avoid -db_hard_mask and -db_soft_mask by changing the class inheritance.
2014-01-16 14:29:50 +00:00
ba5cff01e7
BLAST+ deltablast wrapper (issue #275 )
2014-01-16 14:29:33 +00:00
956c66a0af
BLAST+ 2.2.29 adds -max_hsps, -sum_statistics
2014-01-16 14:09:21 +00:00
14977ce666
Apply 2to3 ws_comma fixer (white space changes)
...
$ 2to3 --no-diffs -n -w -f ws_comma Bio BioSQL Tests Doc Scripts
2013-10-05 13:59:54 +01:00
