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Update compare fasta files #461

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Update compare fasta files #461

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b470376
seperate seq_region comp and fasta
Dishalodha Dec 18, 2024
0d8432d
clean the file
Dishalodha Dec 18, 2024
afbbf27
call the class properly and add args
Dishalodha Dec 18, 2024
43f9350
output a report
Dishalodha Dec 18, 2024
0bc7e9e
add common and only1,only2 to report
Dishalodha Dec 18, 2024
b6241db
add docs
Dishalodha Dec 18, 2024
a4cc52e
updated the logic for check_N and find common
Dishalodha Dec 19, 2024
5a2975c
add docstrings
Dishalodha Dec 19, 2024
e01e554
used black,mypy and moved file to io
Dishalodha Dec 19, 2024
dc0c25e
convert into a module
Dishalodha Dec 19, 2024
10589b9
add license
Dishalodha Dec 23, 2024
9861980
create test for build_seq_dict
Dishalodha Dec 24, 2024
ffac97c
creating test for compare_seq_N
Dishalodha Jan 6, 2025
19d0f94
add test for test_compare
Dishalodha Jan 9, 2025
608d6a6
add test for read fasta
Dishalodha Jan 9, 2025
4be7174
add test for test_write_results
Dishalodha Jan 9, 2025
ff5de2d
add test for test_parse_args
Dishalodha Jan 9, 2025
324fbe3
run black and mypy
Dishalodha Jan 9, 2025
269e140
update seqgroup
Dishalodha Jan 9, 2025
3edb4be
remove compare_fasta from runnable
Dishalodha Jan 9, 2025
0f0b2a7
Apply suggestions from lahcens code review
Dishalodha Jan 27, 2025
3d66dcb
change fasta arg names
Dishalodha Jan 27, 2025
8ba1d56
make the comp list unique
Dishalodha Jan 29, 2025
6b02c9b
correct pylint for compare.py
Dishalodha Jan 29, 2025
0182780
run black and correct pylint
Dishalodha Feb 4, 2025
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1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,7 @@ events_format = "ensembl.io.genomio.events.format:main"
# Fasta
fasta_chunk = "ensembl.io.genomio.fasta.chunk:main"
fasta_process = "ensembl.io.genomio.fasta.process:main"
fasta_compare = "ensembl.io.genomio.fasta.compare:main"
# GenBank
genbank_download = "ensembl.io.genomio.genbank.download:main"
genbank_extract_data = "ensembl.io.genomio.genbank.extract_data:main"
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