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Add Phigaro? #88
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ah yep, you were faster, thanks for the interest and suggestion :) |
@chris-rands the most time-consuming part is writing a parser for the tools and check/validate the tool output
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Hello, I am the Phigaro dev. I wanted to ask, what do you mean when you say contigs? Is it something that you transform initial data in? or is it a prophage region which phigaro detects? |
hi, thank you for the interest. I mean fasta entries/names in a multifasta file. WtP reports which of these fasta entries are phages. It would help if you could give us a good "best practice" command to identify which fasta contains phages/prophages. we could then include phigaro a bit more conveniently for us :) |
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Oh! WTP just finished the work (with a ruin((( ) but still, it managed to produce some data, so do I understand correctly that you need a file like those in a folder |
ad.1 glad to hear its working ad.2 this information is currently not needed but as it seems useful, I think we will add that too at some point (i keep that in mind for now). the complete "raw tool output" is either way completely stored too so the User can check specifically the output from your tool if they want to ad.3. no, we don't need a specific output files, can be any file e.g. output.txt ( we need to rename it either way). This needs to contain a list of header names, without ">", one fasta header name per line (unmodified from the original input) e.g.: fasta_1
fasta_2
fasta_5 yep you can use https://github.com/mult1fractal/WtP_test-data Thank you very much |
Ok, I understand! Thank you very much for your responses))) |
Hello,
By the way, I noticed that What_The_Phage changes the names of the phage positive sequences - at least it replaces the last dot with a dash. But Phigaro does not change anything, as you asked.
Please, let me know if you have any problems or you need something) |
Hej, |
@PollyTikhonova : Phigaro is basically fully integrated into WtP considerations:
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@mult1fractal, Very happy to hear that! We'll wait for your release)))
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No Problem I can take care of it 👍
Database:
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@PollyTikhonova e.g.
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While the wtp option Phigaro is working in its basic mode, so the thresolds for the final score are Briefly, the final score is computed as a product of phage concentration score and triangled GC content score [each of the scores were filtered by indicator function]. |
Thank you very much:) |
Nice tool and idea. Perhaps our phigaro tool could also be included (although I appreciate that adding new tools is probably not trivial):
https://academic.oup.com/bioinformatics/article/36/12/3882/5822875
https://github.com/bobeobibo/phigaro
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