Bio.SearchIO.InterproscanIO package

Submodules

Bio.SearchIO.InterproscanIO.interproscan_xml module
- InterproscanXmlParser
  - InterproscanXmlParser.__init__()
  - InterproscanXmlParser.__iter__()

Module contents

Bio.SearchIO support for InterProScan output formats.

This module adds support for parsing InterProScan XML output. The InterProScan is available as a command line program or on EMBL-EBI’s web page. Bio.SearchIO.InterproscanIO was tested on the following version:

versions: 5.26-65.0 (interproscan-model-2.1.xsd)

More information about InterProScan are available through these links: - Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998142/ - Web interface: https://www.ebi.ac.uk/interpro/search/sequence-search - Documentation: https://github.com/ebi-pf-team/interproscan/wiki

Supported format

Bio.SearchIO.InterproscanIO supports the following format:

XML - ‘interproscan-xml’ - parsing

interproscan-xml

The interproscan-xml parser follows the InterProScan XML described here: https://github.com/ebi-pf-team/interproscan/wiki/OutputFormats

Object	Attribute	XML Element
QueryResult	target	`InterPro`
	program	`InterProScan`
	version	`protein-matches.interproscan-version`
Hit	accession	`signature.name`
	id	`signature.ac`
	description	`signature.desc`
	dbxrefs	`IPR:entry.ac` `go-xref.id` `pathway-xref.db:pathway-xref.id`
	attributes [‘Target’] [‘Target version’] [‘Hit type’]	`-match` / `-location` `signature-library-release.library` `signature-library-release.version`
HSP	bitscore	`*-location.score`
HSP	evalue	`*-location.evalue`
HSPFragment (also via HSP)	query_start	`*-location.start`
	query_end	`*-location.end`
	hit_start	`*-location.hmm-start`
	hit_end	`*-location.hmm-end`
	query	`sequence`

InterProScan XML files may contain a match with multiple locations or multiple matches to the same protein with a single location. In both cases, the match is uniquely stored as a HIT object and the locations as HSP objects.

HSP.*start == *start - 1 (Since every start position is 0-based in Biopython)

HSP.aln_span == query-end - query-start

The types of matches or locations (eg. hmmer3-match, hmmer3-location, coils-match, panther-location) are stored in hit.attributes[‘Hit type’]. For instance, for every ‘phobious-match’, there will be a ‘phobious-location’. Therefore, Hit.type will store the string excluding ‘-match’ or ‘-location’ (‘phobious’, in this example).