[Bioperl-l] GenBank files CONTIG line

Fields, Christopher J cjfields at illinois.edu
Wed Sep 17 13:59:36 UTC 2014


That’s particularly odd; the problem pops up after that commit was added?  

Would it be possible for you to post a bug report on GitHub issues about this?


If this is involving anything other that a simple next_seq/write_seq loop (e.g. if you are doing any additional data manipulation) it would also help to see example code so we can replicate this; once that is in place we can work on bisecting down the problematic commit.


On Sep 16, 2014, at 4:16 PM, Matthew Laird <lairdm at sfu.ca> wrote:

> Good afternoon,
> I wanted to report what I think is an issue but I'm not positive yet.  I found this old mailing list posting from May (http://lists.open-bio.org/pipermail/bioperl-l/2014-May/071583.html) about the changes to NCBI's genbank files, and I just grabbed the latest bioperl live with August's patch to hopefully solve it.  That part worked great, instead of spewing a few GB of warns and the whole sequence multiple times it read the genbank file and wrote out an embl file perfectly fine.
> However the current bioperl live created a new issue.  I have a mirror of NCBI's bacterial genomes directory (yes, I know, I need to move to the new directory structure in the next 6 months) and this pipeline takes the genbank file and makes the embl, ptt, faa, and fna as needed.  This usually takes seconds.  Whatever changed in bioperl live compared to BioPerl 1.6.922 causes the script to spin doing something very intensely for tens of minutes, slowly writing out the ptt file.
> Simply copying genbank.pm from bioperl live to my install directory solved both the CONTIG issue and kept the whole conversion process speedy.  So I'm happy for now, but I wanted to mention this in case it rings a bell with anyone on what could have changed to make parsing a gbk in to a ptt so much less efficient now.
> Thanks.
> -- 
> Matthew Laird
> Lead Software Developer, Bioinformatics
> Brinkman Laboratory
> Simon Fraser University, Burnaby, BC, Canada
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