(Question) provide GFF file for pre computed gene calls?
Opened this issue · 5 comments
Let's say you already ran prodigal and/or have gene calls in GFF format, can you skip the prodigal run and provide the GFF file?
antiSMASH provides a similar option since it requires gene calls and positions but allows for precomputed GFF file to be used.
Just checking it in to see how difficult this would be to implement in the current code base?
Hi. This is available in the dev branch. I will soonish try to get it in the released branch, but until then you can clone this repo and install the dev branch
Thank you! I will try it out.
Just in case it's useful for anyone:
git clone --branch dev https://github.com/Russel88/CRISPRCasTyper.git
pip install CRISPRCasTyper/
I'm testing this out and will log any useful developmental information here:
Here's my usage:
cctyper --db ${CCTYPER_DB} --prodigal single --threads 4 --prot ${PROTEINS} --gff ${GFF} $FASTA $OUT_DIR
- I got an error in the plot module but this resolved it:
try:
import drawSvg as draw
except ModuleNotFoundError:
import drawsvg as draw
Also need to change this:
try:
self.im.saveSvg(self.out+'plot.svg')
except AttributeError:
self.im.save_svg(self.out+'plot.svg')
and this:
try:
self.im.savePng(self.out+'plot.png')
except AttributeError:
self.im.save_png(self.out+'plot.png')
This is because of the update in drawsvg:
https://github.com/cduck/drawsvg?tab=readme-ov-file#upgrading-from-version-1x
-
It looks like the following blast intermediate files aren't removed:
Flank.*
-
The plots are not generated.
total 5.4M
-rw-r--r-- 1 jespinoz users 795 Jan 30 23:37 arguments.tab
-rw-r--r-- 1 jespinoz users 5.5K Jan 30 23:41 blast.tab
-rw-r--r-- 1 jespinoz users 916 Jan 30 23:41 cas_operons_orphan.tab
-rw-r--r-- 1 jespinoz users 12K Jan 30 23:38 cas_operons_putative.tab
-rw-r--r-- 1 jespinoz users 2.2K Jan 30 23:38 cas_operons.tab
-rw-r--r-- 1 jespinoz users 387 Jan 30 23:41 CRISPR_Cas.tab
-rw-r--r-- 1 jespinoz users 962 Jan 30 23:41 crisprs_all.tab
-rw-r--r-- 1 jespinoz users 38K Jan 30 23:41 crisprs.gff
-rw-r--r-- 1 jespinoz users 708 Jan 30 23:41 crisprs_near_cas.tab
-rw-r--r-- 1 jespinoz users 299 Jan 30 23:41 crisprs_orphan.tab
-rw-r--r-- 1 jespinoz users 297 Jan 30 23:41 crisprs_putative.tab
-rw-r--r-- 1 jespinoz users 1.4M Jan 30 23:38 Flank.fna
-rw-r--r-- 1 jespinoz users 20K Jan 30 23:38 Flank.ndb
-rw-r--r-- 1 jespinoz users 5.3K Jan 30 23:38 Flank.nhr
-rw-r--r-- 1 jespinoz users 904 Jan 30 23:38 Flank.nin
-rw-r--r-- 1 jespinoz users 464 Jan 30 23:38 Flank.njs
-rw-r--r-- 1 jespinoz users 788 Jan 30 23:38 Flank.not
-rw-r--r-- 1 jespinoz users 344K Jan 30 23:38 Flank.nsq
-rw-r--r-- 1 jespinoz users 16K Jan 30 23:38 Flank.ntf
-rw-r--r-- 1 jespinoz users 264 Jan 30 23:38 Flank.nto
-rw-r--r-- 1 jespinoz users 383K Jan 30 23:37 genes.tab
drwxr-xr-x 2 jespinoz users 38K Jan 30 23:38 hmmer
-rw-r--r-- 1 jespinoz users 0 Jan 30 23:37 hmmer.log
-rw-r--r-- 1 jespinoz users 109K Jan 30 23:38 hmmer.tab
-rw-r--r-- 1 jespinoz users 11K Jan 30 23:38 minced.out
-rw-r--r-- 1 jespinoz users 3.0M Jan 30 23:37 proteins.faa
drwxr-xr-x 2 jespinoz users 6.0K Jan 30 23:38 spacers
It looks like the following blast intermediate files aren't removed:
Flank.*