Comments (5)
Russel88
commented on June 12, 2024
1
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
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jolespin
commented on June 12, 2024
Just checking it in to see how difficult this would be to implement in the current code base?
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jolespin
commented on June 12, 2024
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/
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jolespin
commented on June 12, 2024
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
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jolespin
commented on June 12, 2024
It looks like the following blast intermediate files aren't removed:
Flank.*
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Related Issues (20)
- FileNotFoundError: blast.tab HOT 3
- Complete genome and draft genome HOT 2
- A complement to CRISRPRCasFinder or its own thing? HOT 1
- Execution against protein fasta and gff HOT 2
- Different results from CRISPR Cas typer web server and standalone version HOT 5
- Error when running cctyper: sed: cannot rename <output filename>/sed78a7GM: Permission denied HOT 2
- 
- Option to use Prodigal-gv
- Meaning of asterisk at the end of protein sequence HOT 1
- Creating empty files when there's no data HOT 1
- castyping.py having an issue with positional arguments. HOT 2
- CCTyper results HOT 4
- Orphan CRISPR definition HOT 2
- XGBoost model incompatible HOT 8
- If minced detects a CRISPR with N's in the repeat sequence
- (Question) How can I plot svg post-hoc after a run? HOT 1
- ValueError: invalid literal for int() with base 10: 'lengt' HOT 2
- access to sequences that used to geenrate Cas profiles
- access to sequences that used to geenrate Cas profiles HOT 1
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