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fix bug related to genbank character limitation #7

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JFsanchezherrero opened this issue Mar 9, 2020 · 2 comments

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JFsanchezherrero commented Mar 9, 2020

In a previous commit, I fixed a bug related to the genbank character limitation of the locus tag that collides the sample name, scaffold and length.

'XXXXX_YYYYYY_229157' generated an exception: Name and length collide in the LOCUS line:
LOCUS XXXXX_YYYYYY_229157_10106259 bp DNA linear 06-MAR-2020

After some googling, this bug (tseemann/prokka#337) appeared where Tseemann already stated the bug and limitations. We set as to 37 character the max length to the fasta headers.
See commit: 26164b5 for details.

Apparently, the bug is still in there and some modifications should be addressed

The text was updated successfully, but these errors were encountered:

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JFsanchezherrero commented Mar 9, 2020

I didnt find any suggestion for the Genbank flat file format that states the character limitation.
https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

General Specifications
ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

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JFsanchezherrero commented Mar 9, 2020

I asked Tseeman about it and to take into account new genbank recommendations
tseemann/prokka#337 (comment)

JFsanchezherrero self-assigned this

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