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Python dev #8

Merged
merged 193 commits into from
Sep 20, 2023
Merged

Python dev #8

merged 193 commits into from
Sep 20, 2023

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bkmarzouk
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Relatively large PR: E2E pipeline runs for SSB192, GH actions in place, along as entry points for genome downloads.

@bkmarzouk
argparse for required inputes
6eb0285
@bkmarzouk
missing required input added
890f3d9
@bkmarzouk
optional args parsing
35f1c5f
@bkmarzouk
promote str input to PosixPath where appropriate
91f5f5f
@bkmarzouk
proto validation check for input paths
47ccd75
@bkmarzouk
pass parsed args to main as kwargs
71580c1
@bkmarzouk
simple check to validate input path
7cb8d08
@bkmarzouk
rename ssb_selection script
c1322a0
@bkmarzouk
ruff cache
fbef219
@bkmarzouk
more type checks on _validate_input_path
43f5489
@bkmarzouk
reduce complexity of checks
695b68a
@bkmarzouk
test _validate_input_path
d85ee60
@bkmarzouk
rename of dest: bed_regions -> target
5a20464
@bkmarzouk
init prepare coordinates
e5bcca6
@bkmarzouk
filter_bed_file_transcript dev
96cca2c
@bkmarzouk
dummy functional methods for stage 2
82d5216
@bkmarzouk
skeleton functions for STEP 2
bcaeca1
@bkmarzouk
rename unit tests dir
4a0ae26
@bkmarzouk
init setup conda py script
aaa2037
@bkmarzouk
init setup conda py script
4d6738d
@bkmarzouk
test config dir
3f192bc
@bkmarzouk
local env yaml
9e306c2
@bkmarzouk
update tests for setup_conda.py
ae9f757
@bkmarzouk
update condarc methods
9563a71
@bkmarzouk
test _create_new_condarc
73754c6
@bkmarzouk
test _update_condarc
2d4aceb
@bkmarzouk
add pytest-dependency
2782cf5
@bkmarzouk
use subprocess to determine conda usage
5ea8f43
@bkmarzouk
init conda env build tests with dependencies
12bf2b9
@bkmarzouk
add dependencies for test_prepare_condarc
7fe1719
bkmarzouk and others added 28 commits September 14, 2023 14:19
@bkmarzouk
_define_variables
dc972bf
@bkmarzouk
implment KaKs computations, define variables and combined quantities,…
bd70b3b 
… etc
@bkmarzouk
_compute_conf_interval
40e6d84
@bkmarzouk
implement confidence and pval computations
6874cdf
@bkmarzouk
dnds calculations in place
7bd81d7
@bkmarzouk
move methods from src/SOPRANO/calculate_KaKsEpiCorrected_Cl_intron.py…
09c100c 
… into dnds.py
@bkmarzouk
move path defs for tcga ssb192 test case into fixture
2ce8bae
@bkmarzouk
Merge pull request #5 from instituteofcancerresearch/step6
2e03fb2 
Step6
@bkmarzouk
add pandas to dependencies file
f925db6
@bkmarzouk
pre-computed fai and chrom files for GRCh37/38 for ensembl release 110
034f4cd
@bkmarzouk
delete old file versions (109)
d85a723
@bkmarzouk
update fixture for change in auxfile which now uses intron file
583d8a6
@bkmarzouk
provide values if assert fails in check_expected_content(...)
08624dc
@bkmarzouk
update directory config and download procedure / pre-processing of ge…
a90bbec 
…nome refs
@bkmarzouk
Update capitalization in ref genomes
3fabf85
@bkmarzouk
add coreutils (GNU) for osx as dependency
262c8c1
@bkmarzouk
generalise downloader & include option to download primary assembly
dcd1eda
@bkmarzouk
add 109 GRCh37 fai and chrom files
884c2d0
@bkmarzouk
add ensemble_transcriptID.translated.fasta index file
2ed8cb7
@bkmarzouk
add fai files for GRCh37/38 rel 110
d2a7998
@bkmarzouk
minor note
387e2f2
@bkmarzouk
homo sapiens vcf inputs (for testing)
e882256
@bkmarzouk
init vep annotation script
f375c35
@bkmarzouk
Merge pull request #6 from instituteofcancerresearch/parse-vcf
cebad7c 
Parse vcf
@bkmarzouk
test workflow tests on macos
ac073ac
@bkmarzouk
update tests to run on osx-actions branch (tmp)
1c6f66e
@bkmarzouk
update workflow files
81bdbbf
@bkmarzouk
Merge pull request #7 from instituteofcancerresearch/osx-actions
c52cbaa 
Mac OS actions
@bkmarzouk
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Tests passed for OS matrix - seems OK.

@bkmarzouk bkmarzouk merged commit 441c278 into python Sep 20, 2023
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@bkmarzouk