Name and length collide in the LOCUS line

tseemann / nullarbor

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Name and length collide in the LOCUS line #208

Closed shimbalama closed 5 years ago

shimbalama commented 5 years ago

Hi Torst,

This happened only ~20 times in 2083 gbks and in only one contig per sample as far as I can tell. When parsing with Biopython I get 'Name and length collide in the LOCUS line:'

Heres an example: LOCUS ERS180486.8898_1_84.11010952 bp DNA linear 21-JUL-2018

I guess you'll just say 'use short names' but maybe you could write something to handle this issue.

tseemann commented 5 years ago

I can't handle it, because the Genbank standard can't encode longer IDs! So Bioperl and every tool in the world will fail to parse it.