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Switch from HIVSeqinR to HIVIntact #23

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Switch from HIVSeqinR to HIVIntact #23

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@Donaim Donaim commented Jul 24, 2023

Closes #10

donkirkby and others added 16 commits July 21, 2023 13:41
@donkirkby @Donaim
Add HIVIntact analysis, for #10.
55536fb
@donkirkby @Donaim
Install mafft and blast in GitHub Actions, for #10.
1d54987
@Donaim
Enable more checks in HIVIntact
6b77cac
@Donaim
Specify writable workdir for hivintact
28ae510
@Donaim
Update dependencies in the README file
9aadb15
@Donaim
Add HIVIntact to our python dependencies
7cfd902
@Donaim
Generate table_precursor table from hivintact output
7f4eba1
@Donaim
Remember intact sequences
891b4a8
@Donaim
Update hivintact errors list
b88c4e4
@Donaim
Improve hivintact errors priority and translation
0bca5be
@Donaim
Bump HIVIntact from cfe-1.2 to cfe-1.3
6ad62bd
@Donaim
Generate proviral_landscape for HIVIntact runs too
7e15cf0
@Donaim
Singularity: make HIVIntact the default and the only app
719a14b
@Donaim
Switch to csv outputs in HIVIntact
a1294df
@Donaim
Rename "hivseqinr_results_tar" argument to "detailed_results_tar"
5c378e9
@Donaim
Bump HIVIntact from 1.3 to 1.4
56d06d9
@Donaim Donaim force-pushed the hivintact-final-results branch from cd0835d to 56d06d9 Compare September 19, 2023 22:13
@Donaim Donaim closed this Mar 6, 2024
@Donaim Donaim force-pushed the hivintact-final-results branch from eae7b0f to 8c55dc3 Compare March 6, 2024 01:42
@Donaim Donaim reopened this Mar 6, 2024
donkirkby
donkirkby reviewed Mar 6, 2024
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We still need approval to actually make the switch, but here are some suggestions for minor code changes.

README.md Show resolved Hide resolved
gene_splicer/utils.py Outdated Show resolved Hide resolved
gene_splicer/utils.py Outdated Show resolved Hide resolved
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Donaim commented Mar 7, 2024

Thanks for review @donkirkby

Base automatically changed from ubuntu1 to master March 7, 2024 17:09
@Donaim Donaim force-pushed the hivintact-final-results branch from 5283b3a to 1c5eca6 Compare July 8, 2024 21:57
@Donaim Donaim force-pushed the hivintact-final-results branch from 36f83e4 to 3d53ae8 Compare July 9, 2024 21:04
@Donaim Donaim force-pushed the hivintact-final-results branch from 136d9b4 to 5fc9340 Compare July 29, 2024 23:34
Donaim added 2 commits July 29, 2024 17:03
@Donaim
Bump pandas version
28950eb
@Donaim
Fix reading of SAM files
6098677 
Instead of using pandas, use the builtin csv module.

Pandas will not parse a SAM file correctly if it does not have regular
number of columns, which some SAM files dont.
@Donaim Donaim force-pushed the hivintact-final-results branch from 29c17d3 to 6098677 Compare July 30, 2024 00:50
@Donaim Donaim force-pushed the hivintact-final-results branch from 92c8d39 to 9f874da Compare December 11, 2024 00:59
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@Donaim @donkirkby