Add genomic coordinates to export_end_sequences and write_fasta headers (2.1.6) - #55
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- export_end_sequences: include strand in the fasta header (chrom:start-end:strand) - write_fasta: new add_coord option to include the genomic location in the header -- the transcript's genomic span for transcript sequences, or the CDS/ORF used for translation for protein sequences - bump biopython/packaging in requirements.txt lock file - bump version to 2.1.6
Dependency Review✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.OpenSSF Scorecard
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Summary
export_end_sequences: include strand in the fasta header (chrom:start-end:strand)write_fasta: newadd_coordoption to include the genomic location in the header -- the transcript's genomic span for transcript sequences, or the coding sequence (annotated CDS, or predicted ORF if not annotated) used for translation for protein sequencesbiopython/packagingin therequirements.txtlock file (drifted since last regenerated)Bumps version to 2.1.6.
Test plan
pytestsuite passes (28 passed, 1 pre-existing unrelated failure deselected)tests/export_test.pycoversadd_coordfor both transcript and protein sequences, and confirms the header is unchanged whenadd_coordis left at its defaultFalseflake8/blackcleanpython -m build+twine check dist/*pass at 2.1.6