Module: rje_busco Description: BUSCO data manipulation library Version: 0.1.2 Last Edit: 10/01/22

Copyright © 2021 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_obj rje_seqlist rje_sequence

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

Function

This module will read in a BUSCO v5 MetaEuk results file and generate the missing *.fna files needed by BUSCOMP. It is designed to be incorporated into BUSCOMP but can be run standalone.

Commandline

Core input/output options

seqin=FILE : Input sequence assembly [None]
basefile=FILE : Root of output file names [$SEQIN basefile]
busco5run=PATH : Path to BUSCO v5 run (e.g. run_SGDR64.2.1/run_saccharomycetes_odb10/) [./]
outdir=PATH : Output directory for reformatted/processed files, if different to [busco5run=PATH]

MetaEuk conversion

metaeukfna=T/F : Perform metaeuk nucleotide busco sequences extraction [False]

History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.1.0 - Added recognition and parsing of transcriptome mode output, which lacks Start and End.
    # 0.1.1 - Fixed bug with sequence names containing pipe characters. (Why?!)
    # 0.1.2 - Fixed bug with odd MetaEuk runs with appended letter on BUSCO ID.