access pathologic via api

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

jo
11 ●7 ●7 ●10

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
561 ●12 ●15 ●24

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
11 ●7 ●7 ●10

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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