===================================================================================
===================================================================================
## Usage
usage: geneLift.py [-h] -cDNA CDNA -g FAA -func ANNOT [-o OUT_P] [-x]
[-aligner ALIGNER] [--report-duplications] [-mm M_PATH]
[-gm GM_PATH] [-c 90] [-i 95] [-t 1]
Script to liftover gene models from reference cDNA alignments
optional arguments:
-h, --help show this help message and exit
-cDNA CDNA fasta file containing transcript sequences
-g FAA Assembly fasta file to lift over gene models
-func ANNOT Semicolon (;) seperated text file with
transcript_id,gene_id,functional annotation for the
cDNA file
-o OUT_P output directory name
-x enable cross species cDNA alignment ; only supported
with aligner gmap
-aligner ALIGNER Aligner used for cDNA alignments options:
[gmap,minimap2]
--report-duplications
Report gene duplications
-mm M_PATH path to minimap2 executable
-gm GM_PATH path to gmap executable
-c 90 Coverage threshold for transcript alignments
-i 95 Identity threshold for transcript alignments
-t 1 Number of threads
To install the dependencies do ( requires conda : https://docs.conda.io/projects/conda/en/latest/ )
git clone https://github.com/srividya22/geneLift.git
cd geneLift
chmod +x ./INSTALL.sh
./INSTALL.sh
$ python setup.py install