Tags: chapmanb/bcbb
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Merge pull request #137 from abretaud/unknownseq Fix error with biopython 1.81
v0.6.8: match records between fasta and GFF with NCBI style headers NCBI PGAP can produce fastas with NCBI headers (`lcl|1`) and GFFs with plain IDs (`1`). This avoids creating duplicate records by matching these and using a consistent contig ID when combining sequences and GFF files. The contig ID used in the final output SeqRecords is the first one encountered. So if you use an external FASTA it's the IDs in the FASTA and if you use a GFF embedded FASTA it's the IDs in the GFF.
Bcbio GFF v0.6.5: Python 3 compatibility; fixes #120
Support Biopython 1.68 with sub_features workaround Biopython deprecated and removed sub_features but the GFF code has not yet put in proper fixes. This works around the issue by adding sub_features when missing so GFF output still works correctly with Biopython >= 1.68. Fixes #110. Fixes biopython/biopython#928
v0.6.2: update version for Python 3 compatibility fixes #96
v0.6.1: Provide Python3 compatibility fixes from @TheOneHyer. Also in… …clude in GFFParser and use six compatibility library for urllib issues. Fixes #90
v0.6: Handle trans-splicing GFF cases where child locations may not m… …atch back to parents. Fixes #91
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