HUGFFF
This is a tool supposed to make it easier for folks to just chuck a modification into a genome.
You need to provide a GFF 3 with sequence in it, and then a genbank formatted construct. Then it takes homology off each end, finds seeds, extends those, then splices together the genome based on those coordinates. Nothing fancy. It's pretty much just BioPython munging. Thanks BioPython!
There's a GFF3 readily available for download from SGD, so it's easy for yeast people.
As seen when you run without arguments.
The only required ones are --referenceGFF which points toward the reference
GFF3 file, --constructGenBank is the genbank file of the thing you are
transforming in, and --output_base is the basename of the new files.
usage: recombinator.py [-h] --referenceGFF REFERENCEGFF --constructGenBank
CONSTRUCTGENBANK [--homology_start HOMOLOGY_START]
[--homology_end HOMOLOGY_END]
[--homology_start_5 HOMOLOGY_START_5]
[--homology_end_5 HOMOLOGY_END_5]
[--homology_start_3 HOMOLOGY_START_3]
[--homology_end_3 HOMOLOGY_END_3]
[--mismatches MISMATCHES] [--mismatches_5 MISMATCHES_5]
[--mismatches_3 MISMATCHES_3] --output_base OUTPUT_BASE
Other parameters deal with tolerable mismatches and adjustable homology on each end of the construct you're trying to transform in.
It's not going to find homology in the middle of the construct, just the very ends of it.
You're going to need BioPython and BCBio. So this can be done with pip,
so pip3 install BioPython and pip3 install bcbio-gff.
If you don't have pip, ... ?