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Published 20 hours ago • verified publisher icon tanghaibao

python -m jcvi.formats.gff fixpartials cost huge memory.

Open xiekunwhy opened this issue 2 years ago • 1 comments

Hi,

Why python -m jcvi.formats.gff fixpartials cost huge memory? Gene number in gff file ~30000(~60000 mRNA, ~19000 are partial). And genome fasta 1.3G

memory

Best, Kun

xiekunwhy avatar Mar 10 '22 05:03 xiekunwhy

@xiekunwhy

this is an uncommon utility in the library and hasn't been worked on for a while. I'd be happy to take a look - would you happen to have a sample gff for me to test? this would help a lot for me to debug this.

tanghaibao avatar Mar 10 '22 19:03 tanghaibao