Nifty tool, thanks! As an FYI, I found a minor issue when using SPAdes-generated draft assemblies to CRISPRDetect, then feeding this .gff output into CRISPR_Studio via conda:
Aligning the spacers with fasta36 aligner
Clustering the spacers
Traceback (most recent call last):
File "/home/sabrina/.conda/envs/bioinfo/bin/CRISPR_Studio", line 855, in
main()
File "/home/sabrina/.conda/envs/bioinfo/bin/CRISPR_Studio", line 808, in main
clDict = attributeClsColor(outFasta+'_fasta36.spacermatch.mcl', spacerDict)
File "/home/sabrina/.conda/envs/bioinfo/bin/CRISPR_Studio", line 248, in attributeClsColor
spacerDict[it].extend([str(colBk), str(colFr), clName])
KeyError: 'NODE_19_length_88379_cov_18.297296||CRISPR1_SPACER1_5446_547'
Shortening the contig names (i.e. to NODE_19) prevents this dictionary failure. I didn't read into the code too closely, but I can see in the KeyError that the CRISPR1_SPACER1 is missing the last digit of the range.
Aloha @moineaulab,
Nifty tool, thanks! As an FYI, I found a minor issue when using SPAdes-generated draft assemblies to CRISPRDetect, then feeding this .gff output into CRISPR_Studio via conda:
Shortening the contig names (i.e. to
NODE_19) prevents this dictionary failure. I didn't read into the code too closely, but I can see in the KeyError that the CRISPR1_SPACER1 is missing the last digit of the range.