|Description:|| RJE MITAB File Parser|
|Last Edit:|| 17/05/16|
Copyright © 2015 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
rje for general commands.
This module is for parsing PPI data from a MITAB file into a pairwise PPI file, using rje_xref.XRef to map protein
sequences onto the KeyID of XRef and a Uniprot field set by
unifield=X. It is best to use an XRef table generated by
PINGU as this includes a "Secondary" field of Uniprot secondary accession numbers.
complex=LIST setting is used to read in iRef-style MITAB files that have complex:XXX identifiers as one of the
interactors. These will be kept during the initial parsing of the file and then replaced with ALL members to generate
a complete set of all-by-all pairwise PPI for the complex.
mitab=FILE : MITAB interaction file 
unifield=X : Uniprot accession number field identifier for xrefdata [
dbsource=X : Source database for evidence field [
idfield=LIST : Gene/protein identifier fields to look for 
mapdb=LIST : Restricted list of database identifier types to try mapping to xref KeyID/MapFields 
taxafield=LIST : Taxon identifier fields to look for 
methodfield=LIST : PPI detection method fields to look for 
typefield=LIST : PPI type fields to look for 
taxid=LIST : List of NCBI Taxa IDs to use [
symmetry=T/F : Whether to impose hub/spoke symmetry on parsed PPI [
complex=LIST : Complex identifier prefixes to expand from mapped PPI [
splicevar=T/F : Whether to allow splice variants in parsed Uniprot identifiers [
unionly=T/F : Whether to restrict PPI to pairwise with UniProt IDs [
adduni=T/F : Whether to add Uniprot IDs that are not returned from mapping file [
History Module Version History
# 0.0.0 - Initial Compilation.
# 0.1.0 - Added complex=LIST : Complex identifier prefixes to expand from mapped PPI [complex]
# 0.1.1 - Fixed Evidence/IType parsing bug for BioGrid/Intact.
# 0.2.0 - Added splicevar=T/F option.
# 0.2.1 - Fixed redundant evidence/itype bug (primarily dip)
rje_mitab REST Output formats
There is currently no specific help available on REST output for this program. Run with
options. Run with
to get full server output. Individual outputs can be identified/parsed:
can then be used to retrieve individual parts of the output in future.