Update src/com/era7/bioinfo/annotation/gb/ExportGenBankFiles.java

[trypsin]

Locus line has one too few spaces after 'LOCUS' before the ID, so that it does not line up with definition/accession/etc. This causes the files to not load properly into Biopython. Additionally adding the linear/circular annotation after the molecule type (DNA) is not genbank-spec, and causes a warning.

[pablopareja]

Hi Jonathan,

Thanks so much for your contribution. Big or small, contributions are
always more than welcome and appreciated ;)
Sorry for taking so long for replying your e-mail but I have been
incredibly busy these past few days.
Regarding the pull request I am replying you through the github pull
requests section.

Cheers,

Pablo

On Thu, Apr 19, 2012 at 1:08 PM, Jonathan <
reply@reply.github.com

wrote:

Locus line has one too few spaces after 'LOCUS' before the ID, so that it
does not line up with definition/accession/etc. This causes the files to
not load properly into Biopython. Additionally adding the linear/circular
annotation after the molecule type (DNA) is not genbank-spec, and causes a
warning.

You can merge this Pull Request by running:

git pull https://github.com/trypsin/BG7 patch-1

Or you can view, comment on it, or merge it online at:

#23

-- Commit Summary --

• Update src/com/era7/bioinfo/annotation/gb/ExportGenBankFiles.java

-- File Changes --

M src/com/era7/bioinfo/annotation/gb/ExportGenBankFiles.java (2)

-- Patch Links --

https://github.com/bg7/BG7/pull/23.patch
https://github.com/bg7/BG7/pull/23.diff

---

Reply to this email directly or view it on GitHub:
#23

[pablopareja]

hehehe I didn't realize that replying to the notification e-mail was the same thing as replying to the pull request here :)
Anyways, I just merged your changes into master.
About the warning, do you know what would be a good alternative for that so that it does not cause a warning anymore?

Pablo

[trypsin]

Sorry, I probably would have tried to fix that too, but I was time crunched actually trying to get annotations for a genome. The problem is that the LOCUS line is defined to have the following format

LOCUS ACCENSION_NUMBER LENGTH bp MOLECULE_TYPE TLA DD-MMM-YYYY

In addition to the missing space after locus BG7 inserts 'LINEAR' or 'CIRCULAR' after MOLECULE_TYPE which some parsers (at least BioPython's SeqIO) will complain and be unable to read the TLA for the data_file_division and the date. I'm not completely sure where the best place to put whether it is circular or linear is, probably in the COMMENT field since its not a specified part of the Genbank flat file format.

Jonathan Goodson
Lab Manager - Winkler Lab
Cell Biology and Molecular Genetics
University of Maryland, College Park
301-405-9937

On Apr 24, 2012, at 9:06 AM, Pablo Pareja Tobes wrote:

hehehe I didn't realize that replying to the notification e-mail was the same thing as replying to the pull request here :)
Anyways, I just merged your changes into master.
About the warning, do you know what would be a good alternative for that so that it does not cause a warning anymore?

Pablo

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Reply to this email directly or view it on GitHub:
#23 (comment)