Enveomics collection

A toolbox for microbial genomics and metagenomics

GFF.catsbj.pl

Generates a list of coordinates from a GFF table concatenating the subject sequences.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

GFF.catsbj.pl [opts] in_file in_file

§ Arguments

Lim file
 -L out_file  An output file with the absolute coordinates of the concatenated contigs. This is identical to the .lim file generated by BlastTab.catsbj.pl.
Inter-feature gaps
 -i   Preserve exact coordinates and include inter-feature windows as separate bins. By default, the coordinates are set in the midpoint between features when non-contiguous.
Subset
 -s   The FastA provided is to be treated as a subset of the subject. By default, it expects all the contigs to be present in the BLAST.
Quiet
 -q   Run quietly.
Subject sequences*
 in_file  Subject sequences (contigs) in FastA format.
Features*
 in_file  Features to map in GFF.
* Mandatory.