VirFinder application in transcriptomes

[denisbruno1]

VirFinder application in transcriptomes

[miasungeunlee]

Hello,
I solved a problem using DeepVIrFinder but still have some problem for predicting q-value from p-value. Waiting her comment on jessieren/DeepVirFinder#6
Try this program, it is more recent.
If it works to you, let me know please :D

Mia

[jessieren]

Hi denisbruno,

Did you solve the problem? If not, could you please send me the command you use? Thanks!

(sorry that I thought I replied your message through emails, but seems not).

Jessie

[miasungeunlee]

Dear Jessie,
Same problem with denisbruno;
Here is the command what i used.

Test run with crAssphage.fasta worked but with my test.fasta file, it doesn't work.

inFaFile <- system.file("data", "crAssphage.fasta", package="VirFinder")
VF.pred(inFaFile)
[1] "crAssphage.fasta [1] line1-1389 gi|674660337|ref|NC_024711.1| Uncultured phage crAssphage, complete genome len 97065 score 0.9826 pvalue 0.0034"
name
1 gi|674660337|ref|NC_024711.1| Uncultured phage crAssphage, complete genome
length score pvalue
1 97065 0.982621 0.003395586
inFaFile <- system.file("data", "test.fasta", package="VirFinder")
predResult <- VF.pred(inFaFile)
Error in countSeqFeatureCpp(seqFa, w) :
Not compatible with STRSXP: [type=NULL].
De plus : Warning message:
In file(inFaFile, open = "r") :
file("") accepte seulement open = "w+" et open = "w+b" : utilisation du premier

Thanks
Best wishes
LEE

[raquelnb]

I had the same problem!

[raquelnb]

Did you guys got the way to solve it?
Thank you!

[raquelnb]

Oh thank you Mia! I'm going to try it out, I'll let you know.
Best

[miasungeunlee]

I re-verified, it worked fine for me too !