66ad0a062e
Extend the .counts method of an Alignment ( #5011 )
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* update
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* halfway finished
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* pdate
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* replace precompiler #defines by inline functions
* update
* update
* add tests
* update
* update
* update
* update
* update
* update
* update
* update
* documentation
* update
* avoid stpcpy
* pointer printing
* compiler warning
* testing without codonalign
* testing without codonalign and pairwisealigner
* compiler warning
* adding codonalign and pairwisealigner back in
* remove inline from check_indices
* add inline to check_indices
* update
* add test line 12287 test_pairwise_aligner.py
* update
* update
* update
* update
* change dtype from int32 to "i"
* all done
* testing
* testing
* testing
* testing
* done
* done
* fix how pointers are printed on Windows
* update
* update
* update
* update
* fix id printing on pypy
* style change only
* Use Py_uintptr_t instead of uintptr_t
* fix memory leak
* remove double semicolon
* check if GitHub actions are now pickup up Python version 3.13.5 without hardcoding it
---------
Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local >
Co-authored-by: Michiel de Hoon <mdehoon@tkx288.genome.gsc.riken.jp >
Co-authored-by: Michiel de Hoon <michiel.dehoon@riken.jp >
2025-07-11 14:40:07 +09:00
e838eb90e6
Generalize the counts attribute of an Alignment ( #4924 )
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* create template
* tests
* tests
* update
* update
* update
* update
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* update
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* stockholm
* update
* update
* update
* update
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* 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
de0bb21fb3
Apply isort (forcing single lines, not sorting by type) via ruff
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$ 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
3c7451b831
Bio.Blast consistent with Bio.SearchIO ( #4617 )
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* hit
* dictionary-like
* update
* undo adding chrom.sizes files
* update
* update
* tests
* repr
* doc
2024-02-11 10:02:34 +09:00
a41e5e3bb8
bugfix ( #4534 )
2023-12-10 11:14:38 +09:00
5c5eaff474
Bio.Align format with target on reverse strand ( #4513 )
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* update
* update
* update
* update
2023-11-26 09:56:11 +09:00
107e308ade
Remove no longer needed flake8 skip commands
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See change to ignore flake8 E131,E122,E124,E126,E127,E128,E201,E241
$ sed -i.bak "/# flake8: noqa$/d" Tests/*.py
2023-11-03 15:11:47 +00:00
e812f38bfb
replace numpy by np in some test scripts ( #4418 )
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* update
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---------
Co-authored-by: Michiel de Hoon <mdehoon@madpc2s-MacBook-Pro.local >
2023-08-14 18:31:48 +09:00
265ffa9532
Bio.Align documentation for bigPsl ( #4411 )
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* update
* update
2023-08-12 17:55:05 +09:00
1add58c797
Bigbed writer ( #4311 )
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* update
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* Fix alignment iterator length calculation
* Update test_Align_bed.py
* Update bed.py
* Update test_Align_bed.py
---------
Co-authored-by: Michiel de Hoon <mdehoon@MichielMacBook.local >
Co-authored-by: Michiel de Hoon <mdehoon@tkx249.genome.gsc.riken.jp >
Co-authored-by: Michiel de Hoon <mdehoon@android-549ef7acc3977720.localdomain >
2023-05-22 04:29:31 +09:00
ae51b5bebd
context manager for Bio.Align.parse ( #4251 )
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* update
* update
2023-03-02 09:35:55 +09:00
340c08af6a
Alignments rewind ( #4246 )
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* update
* update
2023-02-28 12:08:07 +09:00
b09394edc5
print alignments when the sequence is unknown ( #4206 )
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* test_Align_a2m
* clustal
* fasta
* msf
* nexus
* phylip
* stockholm
* stockholm
* maf
* emboss
* hhr
* mauve
* bigmaf
* psl
* bed
* sam
* update
* _get_row
* column
* slice
* tests
* shape
* update
* aligned
* update
* indices
* substitutions
* cleanup
* tests
* tests
* tabular
* update
* update
* update
* update
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* update
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* substitutions
* cleanup
2022-12-30 23:37:03 +09:00
3ddc53fc7e
Alignment str ( #4145 )
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* update
* update
* update
* update
* update
* introduce fixed column size
* expand to multiple alignments
* add tests
* add names
* update
* fix tutorial
* add docstring to explain the coordinates
2022-11-15 09:46:09 +09:00
24286857b9
numpy.array on alignment objects ( #4114 )
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* array
* adding tests
* tests
* tests
* tests
* test
* tests
* tests
* tests
* tests were failing when run through run_tests.py
* test
* test
* test
* test
* test
* test
* test
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* test
* test
* test
* test
* test
* fix test
* update
* update
* finished
2022-10-05 21:04:26 +09:00
518c4be6ae
Alignment format ( #4082 )
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* a2m
* bed
* clustal
* exonerate
* fasta
* maf
* mauve
* nexus
* phylip_psl
* sam
* stockholm
* finished
2022-09-18 20:12:00 +09:00
95393f67a3
add parse, read, write functions to Bio.Align ( #4065 )
2022-08-31 09:40:24 +09:00
714fe3468c
store targets as list ( #4043 )
2022-08-19 10:34:22 +09:00
0dbedd5843
SAM format parser for Bio.Align ( #3872 )
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* starting SAM parser
* starting SAM parser
* add parser
* adding tests
* targets
* writer
* read query sequence from SAM file
* add some mismatches
* add MD tag
* parse optional tags
* read MD
* parse cigar first
* write md tag
* black
* black
* black
* sambam
* black
* flake
* cleanup
* easier
* update
* cleanup
* cleanup
* update
* update
* cleanup
* cleanup
* update documentation
* adding tests
* use soft-clipping for local alignments
* update
* black silliness
* update
* update
* update
* update
* update
* update
* update
* update
2022-06-06 21:01:36 +09:00
