Scripts to help InterPro and Pfam curation, this project has multiple modules
Python 3.6 and above
The scripts are available under the proteome_count subdirectory
Pipeline to search proteins for a given organism or taxid in InterPro signatures.
If unintegrated: search in unintegrated InterPro signatures or cluster proteins using UniRef50 (UniProt)
Usage: python proteome_count/search_proteome.py config.ini [-o ORGANISM | -t TAXID]
Script to search the number of integrated InterPro entries for a given reference proteome, organism or taxid in a given period of time
Usage: python proteome_count/count_all_proteome.py config.ini [-r REF_PROTEOME | -t TAXID | -o ORGANISM]
Script to search the number of integrated InterPro entries corresponding to the key proteomes from the InterPro/Pfam BBR grant in a given period of time
Usage: python proteome_count/count_all_proteome.py config.ini [-r taxid | proteome]
The scripts are available under the pfam_deduf subdirectory
Usage: python pfam_duf/deduf_main.py config_pfam.ini [-o OPTION]: 1)search swissprot names for unintegrated pfam DUF 2)search for DUF in literature 3)search GO term/keywords in Swissprot matches 4)search predicted structures
The scripts are available under the cogs_analysis subdirectory. More details are provided in the corresponding README file.
This script searches for assigned names to CATH-Gene3D signatures not yet integrated in InterPro.
Usage: python search_new_CATH_names.py -u USER -p PASSWORD -s DB_SCHEMA -f INPUTFILE -o OUTPUTFILE [-c COMMENTFILE]