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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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`.complete` method of `Transcript` class return a wrong result for some transcript ids. #252

Open y9c opened 3 years ago

y9c commented 3 years ago

https://github.com/openvax/pyensembl/blob/48bc7ebd12815fcda4f9a3f4e02f3da0a03be510/pyensembl/transcript.py#L421

Minimum example.

cress_genome = pyensembl.Genome(
    reference_name="TAIR10",
    annotation_name="Arabidopsis_thaliana",
    gtf_path_or_url="./Arabidopsis_thaliana.TAIR10.genome.gtf",
    transcript_fasta_paths_or_urls="./Arabidopsis_thaliana.TAIR10.transcriptome.fa",
    protein_fasta_paths_or_urls="./Arabidopsis_thaliana.TAIR10.pep.all.fa.gz",
)

print(gene.transcripts[0].complete)