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Interproscan results parsed into a PGDB

asked 2017-06-16 18:17:24 -0500

anonymous user


Is there a preferred way to parse in interproscan results into a PGDB? I ran all of my bug's proteins against a local installation of interproscan and have a 80MB XML file that I would like to parse in. I could convert it into a tsv, JSON, GFF3 file. I prefer not to write another parser to stuff the interproscan results into a GenBank file and rebuild the PGDB from scratch. Suggestions?

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answered 2017-07-17 15:37:54 -0500

ptools-admin gravatar image

Pathway Tools provides a number of different import/export tools (see Chapter 5 of the User Guide under Help > User Guide). We don't explicitly have support for Interproscan but may provide an import mechanism using one of the import tools outlined in chapter 5. If the information in Chapter 5 doesn't answer your question, please send a detailed email to ptools-support outlining what types of data you need to import.

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Asked: 2017-06-16 18:17:24 -0500

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Last updated: Jul 17 '17