2.9. Loading InterproScan results

In order to load an InterproScan results file, both the query and the subject records must be previously stored. The current version was tested for loading InterproScan analysis on proteins.

2.9.1. Load InterproScan subject records

python manage.py load_similarity_matches --file interproscan_result.xml --format interproscan-xml
  • Loading this file can be faster if you increase the number of threads (–cpu).

2.9.2. Load InterproScan similarity

python manage.py load_similarity --file interproscan_result.xml --format interproscan-xml --so_query polypeptide --so_subject protein_match --program interproscan --programversion 5 --organism_query 'Oryza sativa' --organism_subject 'multispecies multispecies'
  • Loading this file can be faster if you increase the number of threads (–cpu).

python manage.py load_similarity --help

–file

InterproScan XML file *

–format

interproscan-xml *

–so_query

Query Sequence Ontology term. (polypeptide) *

–so_subject

Subject Sequence Ontology term. (protein_match) *

–organism_query

Query’s organism name. eg. ‘Oryza sativa’. Cannot be ‘multispecies’. *

–organism_subject

Subject’s organism name eg. ‘Oryza sativa’. Put ‘multispecies multispecies’ if using a multispecies database. *

–program

Program *

–programversion

Program version *

–name

Name

–description

Description

–algorithm

Algorithm

–cpu

Number of threads

* required fields

2.9.3. Remove file

If, by any reason, you need to remove an InterproScan result set you should use the command remove_analysis.

python manage.py remove_analysis --help
  • This command requires the analysis name (Analysis.sourcename)