ERROR when ">" appears in a gene name

[chartl]

The output of gene prediction algorithms (Prokka) can include ">" characters as part of the gene name, for instance:

>BOGOCDKJ_04879 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase

Currently, BURST checks that the number of ">" characters globally is exactly twice the number of newline characters. Thus, well-formatted FASTA files can throw an error.

[GabeAl]

Thanks for the report! Yes, this is a known issue. BURST also doesn't support multi-line fasta files. Currently I would recommend linearizing the fasta file as well as ensuring that there are no embedded ">" characters in the filename. One way to do this is to name them something arbitrary (like a numeric index) and downstream expand this index into the original name. Another option would be to use "tr" or something to remove all instances of ">", then add them back to every other line (or removing all but the first ">" on every other line, etc). I will keep this issue open as I may have time to work on it. Most systems are I/O bottlenecked, and this was implemented as a speedup technique that indeed causes problems in cases like this. Cheerio, Gabe

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On Tue, Nov 26, 2019 at 3:07 PM chartl ***@***.***> wrote: The output of gene prediction algorithms (Prokka) can include ">" characters as part of the gene name, for instance: >BOGOCDKJ_04879 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase Currently, BURST checks that the number of ">" characters globally is exactly twice the number of newline characters. Thus, well-formatted FASTA files can throw an error. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#21?email_source=notifications&email_token=AB5NOBUVERCJSWUO2J7IVZDQVV6XLA5CNFSM4JR5GGXKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H4HCJCA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5NOBVFXKXKOBSBBCN5LBDQVV6XLANCNFSM4JR5GGXA> .