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
- Perl.
§ 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.