Closed metageni closed 4 years ago
Regarding the last point,
I believe that that prophage.tbl seems to contain the contig name, start and stop for the phage genome rather than the phage genes, right?
The tool takes a gbk file as input. I believe that most people that have a gbk would also have a FASTA file. I know that the tool does not take the FASTA file, but maybe the user could optionally pass it (if wanted) and a FASTA output file with be generated with the phages' genomes. I'm thinking about the end-user who does not know how to parse a FASTA file to get the phage regions. If the program does it, I'm sure people will love it.
We currently require a GenBank
file as we base some of the decisions on the annotations, of course. There are lots of ways to convert a fasta
file to an annotated GenBank
file. We like the PATRIC service or PROKKA for standalone annotation. (Perhaps these are worthy of a http://onestopdataanalysis.com/ blog post!
We are also providing GenBank
format output now.
All other suggestions have been implemented!
Thanks
Hi PhiSpy team, I contacted @linsalrob directly and he told me to write my feedback here.
1)
I noticed that whenFixed by @linsalrob 2/24/20Phispy v3.4.5
is installed, it adds to the pathPhipy.py
, but it also addsPhispy
andphispy
(which don't work). It can be a little misleading even for someone who read theREADME.me
. I think this is a simple fix in the setup.py file.2)
Fixded by @linsalrob 5/20/20prophage.tbl
has two definitions in the README.md file: One states two columns without a header (the one that show in the output), and 2) it shows the file with a header and nicely split into three columns. I believe the second one if possible would be nice to have.3)
The README states thatIf the column contains a 0 we believe that it is a bacterial gene
and in another section it says:If this column is 1 then the gene is a phage like gene; otherwise it is a bacterial gene.
It is a little ambiguous to understand what it is when value > 1. I believe >=1 is a phage region - I saw some regions annotation with "phage" as substring and column 10th > 1. Maybe clarify the README.me.Fixded by @linsalrob 5/20/204)
AddFixed by @linsalrob 2/24/20scikit-learn >=0.21.3
toSoftware Requirements
. I believe numpy is not showing because it will be installed when installing Biopython ?!5) I believe that that
prophage.tbl
seems to contain the contig name, start and stop for the phage genome rather than the phage genes, right?The tool takes a gbk file as input. I believe that most people that have a gbk would also have a FASTA file. I know that the tool does not take the FASTA file, but maybe the user could optionally pass it (if wanted) and a FASTA output file with be generated with the phages' genomes. I'm thinking about the end-user who does not know how to parse a FASTA file to get the phage regions. If the program does it, I'm sure people will love it.
I'm working in a blog post (http://onestopdataanalysis.com/) which will be posted a few months from now on how to go from bacterial FASTA to phage FASTA (Docker image with prokka and phispy, use the phispy output to and parse the phages FASTA file).
I will write a script to do the parsing and would be more than happy to add to the code base if given access. Otherwise, I'm also happy to share it with the team.
Thanks