Formatting of genome fasta file for specifying target seq regions

[cgstorer]

Hello Trinh Lab (and perhaps Brian?),

I am hoping to use CASPER for target design and off-target analysis. I have a draft non-public genome, where each contig is named in the following format ">12 edges=6838..105895 left=15722 right=84164 ver=1.9 style=3".

Using the CASPER_Seq_Finder executable I am able to successfully generate all possible target sequences and the resulting .cspr file which looks like this:

head pinspCas9.cspr

0 edges=152165..156910 left=47242 right=79982 ver=1.9 style=3 (1)
g,|Hc8llRZ-9,r
m,|MllRZFk-z,d
o,|JZUWRZM-8,e
p,|FlRZFkw-y,g
x,|EDDaYgp+w,h
2,|EwQMNpi+w,n
B9,|PUA1ESF-z,o
CW,|EEHREJV+w,h
Cy,|J5VrLol-w,h

I am interested in only looking for targets for specific known exons on a single contig/chromosome so I edited Run_CASPER.py as follows.

run = "CASPERQuick"

---------- GENERAL SETTINGS ------------------

These settings are needed for all Analyses

CASPER_Seq_Finder_files_directory = "/Users/xxx/Desktop/xxx/CRISPR_DB/"
output_file_path = "/Users/xxx/Desktop/xxx/CRISPR_DB/"
endonuclease = 'spCas9' # This is for the output file name
base_organism_code = "pin" # use the KEGG code that was used to name your CASPER_Seq_Finder file

---------- SPECIFIC SETTINGS ------------------

Settings specific for CASPERQuick:

regions_or_kegg_codes = ["12,1451967,1452086"]
off_target_all = False

However, I get the following error

python Run_CASPER_CASPERQuick_xxx_Seg1.py
Traceback (most recent call last):
File "Run_CASPER_CASPERQuick_xxx_Seg1.py", line 48, in
C.loadGenesandTargets(regions_or_kegg_codes)
File "/Users/xxx/Desktop/xxx/CASPER_master/CASPERQuick.py", line 29, in loadGenesandTargets
self.location = k.gene_locator(region_kegg)
File "/Users/xxx/Desktop/xxx/CASPER_master/CASPERQuick.py", line 71, in gene_locator
newstr = d['POSITION']
TypeError: 'int' object is not subscriptable

Perhaps, there is something simple that I am missing about the genome fasta formatting or specifying regions for target design?

Any help you can offer would be greatly appreciated.

Best, Caroline