PhiSpy
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linsalrob
Prediction of prophages from bacterial genomes
Hello, PhisPy process errors out and doesn't produce results file - confirmed same behavior on both separate venv & pip installation and conda environment installation. Attaching error message (this one...
Hi! I'm encountering a problem when running phispy (conda environment) with the provided test files. The analysis runs with no problems and I can see that it identifies prophages but...
hello，I am using a docker image to install Phispy 4.2.21，but the glibc version of base image is 2.35，so I can‘t install it ，is there any pre-build phispy or other method...
There is a small issue where one of the biopython functions has a character length limit on sequence IDs, a more informative error message might be useful. A fasta ID...
### The following is the code I ran and the error situation. Has anyone encountered this issue? BioPython version is 1.77, and PhiSpy version is 4.2.21 (PhiSpy) [kxy@zju out]$ PhiSpy.py...
Dear Rob, I am currently using PhiSpy version 4.2.21 to detect prophages in several strains of Aeromonas and, for one of them (that is available at the NCBI: https://www.ncbi.nlm.nih.gov/nuccore/CP043323.1/) and...
The sequences of att site and prophage region in the output files decrease a base comparing with the sequences we extracted by positions in outfiles.So,which is the correct result?Thank you.
Hello, I occasionally run into this issue when running PhySpy: ``` 2022-03-28 12:14:53 INFO Welcome to PhiSpy.py version 4.2.21 2022-03-28 12:14:53 INFO Starting PhiSpy.py with the following arguments Namespace(infile='input/genomic.gbff', output_dir='/home/ec2-user/physpy',...
Would it be possible to add all the features detected by phispy (att sites mostly) to the GFF3 format? They can be quite useful for visualization in certain software liek...
Hi, I am using PhiSpy to predict prophages from bacteria. But the prophage fasta file have been masked with Ns. You say it is trivial to convert this format into...
