PhiSpy
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linsalrob
Prediction of prophages from bacterial genomes
Extract the locations from these genomes and add them to our GenBank files as appropriate: http://phaster.ca/statistics#table4
Very often contig breaks in draft genomes occur within prophages. This is because the prophage contains repeat regions (like IS elements), the prophage has unusual coverage (e.g. because it is...
I noticed that the below check forces users to keep their retrained reference datasets in INSTALLATION_DIR/PhiSpyModules/data directory https://github.com/linsalrob/PhiSpy/blob/540fbf2548cd6580a6fd9d0a8e003226b1044710/PhiSpyModules/classification.py#L34-L36 The same will happen with kmers file within makeTest.py and makeTrain.py https://github.com/linsalrob/PhiSpy/blob/540fbf2548cd6580a6fd9d0a8e003226b1044710/PhiSpyModules/makeTest.py#L16-L20...
There is an issue when I run PhiSpy on *.gbk files obtained by Prokka, I don't know why. $ PhiSpy.py -o outfile *.gbk error message: Traceback (most recent call last):...
Hi @linsalrob and team, Thanks for the great tool! We were trying to use it on https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/033/802/525/GCF_033802525.1_ASM3380252v1/GCF_033802525.1_ASM3380252v1_genomic.gbff.gz Interestingly, we got slightly different results with PhiSpy, PhiSpy (PHROGs - used `sed...
Thanks for the interesting and useful tool! Hit this error on the following file, running v4.2.21 from bioconda. ```bash wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/035/013/225/GCA_035013225.1_ASM3501322v1/GCA_035013225.1_ASM3501322v1_genomic.gbff.gz gunzip GCA_035013225.1_ASM3501322v1_genomic.gbff.gz PhiSpy.py -o test --threads 2 --output_choice 4...