127b7ced69
Added cmsearch and cmscan result files for testing
2025-03-22 06:59:36 +01:00
9b5a6a7c76
Automatically infer the tabular format from the header
2025-03-22 06:59:36 +01:00
3ff3c8696a
Fixed docstring
2025-03-22 06:59:36 +01:00
fde0575a06
Added testing for notextw plain text output
2025-03-22 06:59:36 +01:00
340069f275
Standardized assertion format
2025-03-22 06:59:36 +01:00
339ed21ebb
Moved model information to the HSP in the tabular format parser
2025-03-22 06:59:36 +01:00
1458c805e4
Fixed issues in text format testing
2025-03-22 06:59:36 +01:00
42770537de
Fixed formatting
2025-03-22 06:59:36 +01:00
c52296697b
Tests names standardization
2025-03-22 06:59:36 +01:00
02b8e418d2
Added infernal text indexer
2025-03-22 06:59:36 +01:00
1b899dd167
Corrected testing function name
2025-03-22 06:59:36 +01:00
dacaa2dce7
Better fmt support in tabular format indexer
2025-03-22 06:59:36 +01:00
05caa75aae
Enhanced spacing
2025-03-22 06:59:36 +01:00
1dcab7face
Added support for tabular output format 3
2025-03-22 06:59:36 +01:00
2d1495692b
Changed tests files names
2025-03-22 06:59:36 +01:00
103e05102e
Added tabular format indexer and related tests
2025-03-22 06:59:36 +01:00
f891b58411
Removed dependency on the header to guess tabular format in preparation for the Indexer
2025-03-22 06:59:36 +01:00
f790c862dc
Added tests for cmscan text output parsing
2025-03-22 06:59:36 +01:00
fb652f742f
Fixed an issue with cmscan tabular file processing
2025-03-22 06:59:36 +01:00
5bbe63f536
Updated counter in cmsearch tabular tests to match cmsearch text output method
2025-03-22 06:59:36 +01:00
ef305bcb17
Added support for cmsearch hits with non-consecutive hits
2025-03-22 06:59:36 +01:00
ca5a44d694
Added tests for cmsearch output with multiple queries
2025-03-22 06:59:36 +01:00
f7c6776bb5
Added support for HMM-only searches
2025-03-22 06:59:36 +01:00
33ca1c3cfa
Added Infernal text output parser and tests
2025-03-22 06:59:36 +01:00
3fa9d17dd4
Added Infernal tabular format parser and tests
2025-03-22 06:59:36 +01:00
f452e2e860
Added cmsearch and cmscan result files for testing
2025-03-22 06:59:36 +01:00
79759c8394
Locale independent date serialization ( #4977 )
...
Locale independent date serialization, also accept datetime.date
Add warning when date is invalid/not in the expected format
Closes #4972
2025-03-21 15:39:57 +00:00
9ba39c2558
Prevent out of bound index to mapping when aligning strings ( #4968 )
...
* update
* update
* update
* update
* update
---------
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-03-11 17:17:53 +09:00
67a37865e5
Retain letter_annotation as None in upper and lower methods ( #4966 )
...
* gitignore .python-version
* added name & email
* fix so that _per_letter_annotations is not set by calling upper or lower methods
* added test for initiation of SeqRecord checking the __dict__ and a test for the __dict__ created by upper
2025-03-10 14:01:25 +00:00
882072e8fe
update ( #4964 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-03-02 09:19:37 +09:00
cc4eec481a
Always use ELLIPSIS option in test_Tutorial.py
...
This now the main docstrings (done via run_tests.py) and their helper
function in Bio/_utils.py
2025-02-28 07:51:11 +00:00
aabf125517
Alignments repr ( #4957 )
...
* update
* update
* update
* update
* black
---------
Co-authored-by: Michiel de Hoon <mdehoon@tkx288.genome.gsc.riken.jp >
2025-02-28 11:32:06 +09:00
57a8bb8732
Bio.Align tabular, avoid next() so we can use NamedTemporaryFile ( #4955 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-25 23:48:42 +09:00
8f27d9efd9
Bio.Align psl, avoid next() so we can use NamedTemporaryFile ( #4954 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-25 22:36:10 +09:00
d4da11fd5a
Bio.Align phylip, avoid next() so we can use NamedTemporaryFile ( #4953 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-25 11:46:42 +09:00
557e1d6503
Bio.Align nexus, avoid next() so we can use NamedTemporaryFile ( #4952 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-25 10:51:07 +09:00
364ca02839
Bio.Align maf, avoid next() so we can use NamedTemporaryFile ( #4950 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-25 09:35:27 +09:00
5d56f900d2
Bio.Align hhr, avoid next() so we can use NamedTemporaryFile ( #4949 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-25 00:04:33 +09:00
d6fcdfa131
Changed several parsers avoid using next.
...
tempfile.NamedTemporaryFiles do not support __next__.
2025-02-24 14:16:22 +00:00
c3c9c736d6
Bio.Align emboss, avoid next() so we can use NamedTemporaryFile ( #4947 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-24 17:46:40 +09:00
bca5545f16
avoid next() so we can use NamedTemporaryFile ( #4946 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-24 17:02:29 +09:00
d60677586a
avoid next() so we can use NamedTemporaryFile ( #4945 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-24 16:07:54 +09:00
775b90182e
fix test
2025-02-19 21:49:09 +00:00
a6bdb14fda
remove unused variable ( #4934 )
2025-02-13 12:11:31 +09:00
9962ca2691
PairwiseAligner attribute names ( #4933 )
...
* target_internal_extend_gap_score
* target_internal_open_gap_score
* target_left_open_gap_score
* self.target_left_extend_gap_score
* target_right_open_gap_score
* target_right_extend_gap_score
* query_left_open_gap_score
* query_left_extend_gap_score
* query_internal_open_gap_score
* query_internal_extend_gap_score
* query_right_open_gap_score
* query_right_extend_gap_score
* target_gap_function
* query_gap_function
* internal_open_gap_score
* left_open_gap_score
* left_extend
* right_open_gap_score,right_extend_gap_score
* end_extend_gap_score
* target_open_gap_score
* target_extend_gap_score
* query_open_gap_score
* target_gap_score
* target_end_gap_score
* target_end_open_gap_score
* target_end_extend_gap_score
* target_internal_gap_score
* target_left_gap_score
* target_right_gap_score
* dc
* query_gap_score,query_extend_gap_score
* query_end_gap_score
* query_end_open_gap_score
* query_end_extend_gap_score
* query_internal_gap_score
* update
* doc
* doctest
* tests
* update
* tests
* tests
* pickle
* tests
* deprecation tests
* documentation
* flake
* black
* deprecated
---------
Co-authored-by: Michiel de Hoon <mdehoon@tkx288.genome.gsc.riken.jp >
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-10 15:25:21 +09:00
6adade16fb
wildcard ( #4931 )
...
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-07 14:46:30 +09:00
4d380fab03
use ignore_sequences instead of gaps_only ( #4929 )
...
* update
* update
* update
---------
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-06 21:44:09 +09:00
e838eb90e6
Generalize the counts attribute of an Alignment ( #4924 )
...
* create template
* tests
* tests
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* stockholm
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
---------
Co-authored-by: Michiel de Hoon <mdehoon@tkx288.genome.gsc.riken.jp >
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
2025-02-04 22:45:43 +09:00
dda590d43f
SeqRecord now requires Seq or MutableSeq ( #4917 )
...
* remove deprecated code
* test now get TypeError
* update deprecated file
2025-01-19 11:11:20 +00:00
b929c3c794
remove deprecated .strand, .ref and .ref_db from Seqfeature ( #4916 )
2025-01-17 11:04:45 +00:00
