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rje_synteny V0.0.3

Gene/Protein Annotation Transfer and Synteny Tool

Module: rje_synteny
Description: Gene/Protein Annotation Transfer and Synteny Tool
Version: 0.0.3
Last Edit: 26/06/17

Copyright © 2016 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_genbank rje_obj rje_seqlist


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

Function

This module is based on the TopHits analysis of PAGSAT. It takes as input: - A Reference Genome sequence [refgenome=FILE]
- A Reference Genome feature table with Gene and CDS features [ftfile=FILE]
- GABLAM search results (e.g. from PAGSAT) of Genes/Proteins against assembly regions [ftgablam=FILE]

Commandline

Input/Output options

refgenome=FILE : Fasta/Genbank file of reference genome for assessment (also *.gb for full functionality) [None]
ftfile=FILE : File of reference genome features [*.Feature.tdt]
ftgablam=FILE : GABLAM search results (e.g. from PAGSAT) of Genes/Proteins against assembly regions [None]
basefile=FILE : Basename for output files [ftgablam basefile]

Processing options

proteins=T/F : Whether input is protein sequences (True) or genes (False) [False]
tophitbuffer=X : Percentage identity difference to keep best hits for reference genes/proteins. [1.0]


History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.0.1 - Altered problematic ValueError to warnLog()
    # 0.0.2 - Updated the synteny mappings to be m::n instead of m:n for Excel compatibility.
    # 0.0.3 - Added catching of the Feature locus/accnum mismatch issue.

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