feature: adding converters and test data for AA translation #87
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* refactor: move lapis script to module * refactor: move wrangleing to silo module * refactor: move wrangleing to silo module * add docs * Update src/sr2silo/silo/wrangle.py Co-authored-by: Copilot <[email protected]> * typos - github copilote Co-authored-by: Copilot <[email protected]> * refactore: moving the URLs for lapis to env variables * bug: auth should not be got is in CI * silo * silo * OO in silo * works * WORKS * CI issue --------- Co-authored-by: Gordon J. Köhn <[email protected]> Co-authored-by: Copilot <[email protected]> Getting all Changes from the Nextclade Try on main for try with BlastX
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Copilot reviewed 13 out of 16 changed files in this pull request and generated 5 comments.
Files not reviewed (3)
- src/sr2silo/process/merge.py: Evaluated as low risk
- src/sr2silo/process/init.py: Evaluated as low risk
- README.md: Evaluated as low risk
Comments suppressed due to low confidence (7)
src/sr2silo/process/convert.py:120
- The dictionary key 'RESULT_seqUENCE' is incorrectly named. It should be 'result_sequence'.
"RESULT_seqUENCE": result_sequence,
src/sr2silo/process/convert.py:71
- The word 'Nuliotide' is misspelled. It should be 'Nucleotide'.
logging.warning("pair_normalize_reads: Nuliotide Insertions are not yet implemented, {output_insertions} will be empty.")
src/sr2silo/process/convert.py:72
- The logging message is missing a format string for '{output_insertions}'.
logging.warning("pair_normalize_reads: Nuliotide Insertions are not yet implemented, {output_insertions} will be empty.")
src/sr2silo/process/convert.py:251
- The 'missing_ok' parameter for 'unlink' is not available in Python versions below 3.8. This could cause compatibility issues.
Path(sorted_bam_path_str + ".bai").unlink(missing_ok=true)
tests/process/test_convert.py:17
- [nitpick] The print statement is unnecessary and should be removed.
print(bam_data)
tests/process/test_convert.py:80
- [nitpick] The variable 'save_to_another_dir' is defined but not used effectively. It should be removed.
save_to_another_dir = False
tests/conftest.py:49
- The variable name 'EXPECTED_BAM_INSERTIONS_PATH_inserts' should be 'EXPECTED_BAM_INSERTIONS_PATH_INSERTS' to follow naming conventions.
EXPECTED_BAM_INSERTIONS_PATH_inserts = (
Co-authored-by: Copilot <[email protected]>
gordonkoehn
changed the title
Co-authored-by: Copilot <[email protected]>
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This PR cherry picks some changes done in
#78
for nextclade to be used in the trial with BlastX.