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Analysis ssb192 #3

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merged 17 commits into from
Sep 12, 2023
Merged

Analysis ssb192 #3

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b9a66d6
fix bug in writing of intra fasta file
bkmarzouk Sep 11, 2023
8a91d5d
estimate subs ssb192
bkmarzouk Sep 11, 2023
f1f4a33
raise runtime error for subprocess steps with non-zero exit
bkmarzouk Sep 11, 2023
5390088
replace buggy method for obtaining transcript:regions
bkmarzouk Sep 11, 2023
1d8b0c1
compute sums over all possible target and non target region sites
bkmarzouk Sep 11, 2023
74cea6e
FixSimulated and ColumnCorrect methods
bkmarzouk Sep 11, 2023
efff3d7
entry point for downloading reference genome files
bkmarzouk Sep 11, 2023
e147154
update parameters to include attribute containing GenomePaths object
bkmarzouk Sep 11, 2023
921cd3c
path fix for ref genomes in frozen data instances
bkmarzouk Sep 11, 2023
7b4503b
Implement context corrections for ssb192
bkmarzouk Sep 11, 2023
d3ad000
add fasta index file for GRCh37
bkmarzouk Sep 11, 2023
f6ecc05
Implement FlagComputations
bkmarzouk Sep 11, 2023
bd58132
Implement TripletCounts
bkmarzouk Sep 11, 2023
329e24d
note in master shell script: code block looks redundent
bkmarzouk Sep 11, 2023
866b824
SiteCorrections
bkmarzouk Sep 12, 2023
fe64f19
typo fix
bkmarzouk Sep 12, 2023
48f16f2
omit integration tests from pipeline (tmp) - these have too many data…
bkmarzouk Sep 12, 2023
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10 changes: 5 additions & 5 deletions .github/workflows/test.yml
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Expand Up @@ -60,8 +60,8 @@ jobs:
run: |
micromamba activate soprano-dev
pytest tests/test_units
- name: Test integration
shell: bash -l {0}
run: |
micromamba activate soprano-dev
pytest tests/test_integrations
# - name: Test integration
# shell: bash -l {0}
# run: |
# micromamba activate soprano-dev
# pytest tests/test_integrations
3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -68,4 +68,5 @@ dmypy.json
src/SOPRANO/tmp/

# Data files
src/SOPRANO/data/ensemble_transcriptID.fasta
src/SOPRANO/data/ensemble_transcriptID.fasta
src/SOPRANO/data/Homo_sapiens.GRCh*.fa
3 changes: 2 additions & 1 deletion pyproject.toml
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Expand Up @@ -52,7 +52,8 @@ Homepage = "https://github.com/instituteofcancerresearch/SOPRANO"
Discussions = "https://github.com/bkmarzouk/symflation/discussions"

[project.scripts]
SOPRANO = "SOPRANO.run_local_ssb_selection:main"
RUN_SOPRANO = "SOPRANO.run_local_ssb_selection:main"
GET_GENOMES = "SOPRANO.run_local_ssb_selection:download_genome"

[tool.hatch]
version.source = "vcs"
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