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rje_mitab V0.2.1

RJE MITAB File Parser

Module: rje_mitab
Description: RJE MITAB File Parser
Version: 0.2.1
Last Edit: 17/05/16

Copyright © 2015 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_obj rje_xref


See SLiMSuite Blog for further documentation. See rje for general commands.

Function

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.

The 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.

Commandline

Input Options

mitab=FILE : MITAB interaction file []
unifield=X : Uniprot accession number field identifier for xrefdata ['Uniprot']
dbsource=X : Source database for evidence field ['mitab']
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 []

Parsing Options

taxid=LIST : List of NCBI Taxa IDs to use [9606]
symmetry=T/F : Whether to impose hub/spoke symmetry on parsed PPI [True]
complex=LIST : Complex identifier prefixes to expand from mapped PPI [rigid]
splicevar=T/F : Whether to allow splice variants in parsed Uniprot identifiers [False]
unionly=T/F : Whether to restrict PPI to pairwise with UniProt IDs [False]
adduni=T/F : Whether to add Uniprot IDs that are not returned from mapping file [True]


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 &rest=help for general
options. Run with &rest=full to get full server output. Individual outputs can be identified/parsed:
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
...

&rest=OUTFMT can then be used to retrieve individual parts of the output in future.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.