missing the DNA fasta output file

[andriangajigan]

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]

It seems that

prodigal -i <genome.fa> -d <nucleotide.fa> -a <prot.faa> -o <genome.gff> -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]

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 <genome.fa> -d <nucleotide.fa> -a <prot.faa> -o <genome.gff> -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 — Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPFN7W4QSYQJCSN32FVUFTYV2BK5AVCNFSM6AAAAABD47XGTCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRYGAYTMMRUGE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[andriangajigan]

Yes. Thanks Frank!