Closed deprekate closed 5 years ago
JFsanchezherrero
commented
5 years ago Hi @deprekate,
I asked a few months ago about this new implementation (#7 ) and as I got no reply, I decided to implement it myself.
I forked your code and generated a few updates and new implementations such as gff and csv output.
https://github.com/JFsanchezherrero/PhiSpy
Please check the code and if you want me to pull a request I can do it. Regards
deprekate
commented
5 years ago Jose
Oh, sorry, I never received any notifications and have been super busy with other programs (shameless plug here for my software PHANOTATE https://doi.org/10.1093/bioinformatics/btz265). Your updates are indeed useful, I will incorporate them into the main branch, once I wade through Rob's working branch and my branch to merge it all.
I am working with Przemysław Decewicz to recreate the training data sets (and add new ones). This actually needed to be done 2 years ago after I fixed the underlying code, since the training data was slightly off (I fixed the calculations that PhiSpy made on the input genome, but did not recreate the training data to match the fixed calculations). My master branch has a new command line arg that will take a genbank genome where the prophage regions are marked with the /is_phage=1 keyword; and then PhiSpy will output a training file. I still have to fix PhiSpy so it will take a filepath as an arg for the training set to use.
Katelyn
On Fri, Aug 23, 2019 at 1:04 AM Jose Francisco Sanchez-Herrero < notifications@github.com> wrote:
Hi @deprekate https://github.com/deprekate,
I asked a few months ago about this new implementation (#7 https://github.com/linsalrob/PhiSpy/issues/7 ) and as I got no reply, I decided to implement it myself.
I forked your code and generated a few updates and new implementations such as gff and csv output.
https://github.com/JFsanchezherrero/PhiSpy
Please check the code and if you want me to pull a request I can do it. Regards
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Updated the code to Python3 (it still works on Python2.7 as well).
Also updated minor cosmetic changes (removing excessive blank lines, etc)