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access pathologic via api

asked 2017-05-17 05:46:02 -0600

jo gravatar image

Is it possible to access pathologic via an API? Would like to create draft models via the pathologic algorithms without using the graphical interface. Could this be done?

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answered 2017-05-17 19:29:30 -0600

quang777 gravatar image

Yes, there's a mode called "Batch Pathologic". Please review section 7.6 of the UserGuide (under Help > User Guide). Batch Pathologic accepts a couple of different input file formats. Please review those options.

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answered 2017-05-18 08:40:07 -0600

jo gravatar image

Thanks for pointing this out!

So I defined organism-params.dat and genetic-elements.dat in a folder called dir_with_files, included the annotation file test.gbk and started pathwatools: pwt -patho dir_with_files

organism-params.dat

ID      test
NAME    Pseudomonas lurida
STORAGE File
NCBI-TAXON-ID   244566
DOMAIN  TAX-2

genetic-elements.dat

ID      TEST-CHROM-1
TYPE    :CHRSM
CIRCULAR?       Y
ANNOT-FILE      test.gbk
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Asked: 2017-05-17 05:46:02 -0600

Seen: 45 times

Last updated: May 18