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faylward / viralrecall

Detection of NCLDV signatures in 'omic data
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missing the DNA fasta output file #26

Open andriangajigan opened 5 months ago

andriangajigan commented 5 months ago

Thank you for creating this tool! Helps me a lot.

I noticed I was missing this output file when I ran ViralRecall: *.fasta: The DNA coding sequence of the predicted proteins from Prodigal

Running, for instance, python viralrecall.py -i bin.10.fa -p bin.10 -t 8 -c

would only give me bin.10.faa bin.10.full_annot.tsv bin.10.markerout bin.10.pfamout bin.10.summary.tsv bin.10.vogout

andriangajigan commented 5 months ago

It seems that

prodigal -i -d -a -o -f gff -p meta

will give the exact same output as the prodigal run in ViralRecall

cmd = "prodigal -p meta -i "+genome_file" -a "+protein_file"

I just need the nucleotide.fa output

faylward commented 5 months ago

Yes - "-a" gives the protein output and "-d" provides the nucleic acid sequence. You have the right command. Does that answer your question?

Frank

On Tue, Feb 27, 2024, 8:23 PM Andrian Gajigan @.***> wrote:

It seems that

prodigal -i -d -a -o -f gff -p meta

will give the exact same output as the prodigal run in ViralRecall

cmd = "prodigal -p meta -i "+genome_file" -a "+protein_file"

I just need the nucleotide.fa output

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andriangajigan commented 5 months ago

Yes. Thanks Frank!