# Bio.SearchIO.InterproscanIO package

## Submodules

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

## 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`
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).

Biopython v: 1.85

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