Module: rje_exonerate Description: Runs Exonerate and parses output Version: 0.5.1 Last Edit: 14/09/18

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

Imported modules: rje rje_db rje_obj rje_seqlist rje_sequence rje_blast_V2

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

Function

The function of this module will be added here.

Commandline

exopt=X : Exonerate options to add. Will split on whitespace. No semicolons allowed. []
memsaver=T/F : Whether to run in memsaver mode that stores exonerate output in intermediate text file [False]
cleanup=T/F : Remove intermediate files after run if memsaver=T [False]
gzip=T/F : Whether to gzip (and gunzip) exonerate results files (not Windows) [True]

History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.1.0 - Initial Working Version
    # 0.1.1 - Fixed no model bug for DNA searches.
    # 0.2.0 - Added SeqList objects to store compiled aligned sequences.
    # 0.3.0 - Added Exonerate Options.
    # 0.4.0 - Added MemSaver mode.
    # 0.4.1 - Fixed bug in GFF output that had ID and Name uniqueness swapped.
    # 0.5.0 - Added QryDesc to GFF output.
    # 0.5.1 - Fixed bug in hitsum combined score.