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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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protein sequence output file #123

Open graciegracekk opened 1 year ago

graciegracekk commented 1 year ago

I'm running the dbcan on faa files on linux to predict the CAZymes and saw that I can get a protein sequence of the gene (this link shows an output of the gene with the protein sequence: https://bcb.unl.edu/dbCAN2/data/blast/20221121163906/CAZyme.pep) . How do I get that ^^output file?

linnabrown commented 1 year ago

Sorry I could not get your point. Could you rephrase ur question?

graciegracekk commented 1 year ago

hi,

  1. I want to get a protein sequence of the CAZyme when I run the dbCAN. How do I get the output file that looks like this? (has the following info)

    NC_000913.3_1054 3.2.1.-:GH73(160-295):GH73_e114:GH73:N:3

MISDSKLLASAAWDAQSLNELKAKAGEDPAANIRPVARQVEGMFVQMMLKSMRDALPKDG LFSSEHTRLYTSMYDQQIAQQMTAGKGLGLAEMMVKQMTPEQPLPEESTPAAPMKFPLET VVRYQNQALSQLVQKAVPRNYDDSLPGDSKAFLAQLSLPAQLASQQSGVPHHLILAQAAL ESGWGQRQIRRENGEPSYNLFGVKASGNWKGPVTEITTTEYENGEAKKVKAKFRVYSSYL EALSDYVGLLTRNPRYAAVTTAASAEQGAQALQDAGYATDPHYARKLTNMIQQMKSISDK VSKTYSMNIDNLF*

2.Can I run dbCAN on both FAA and FNA files? or is it just FNA files?

Grace

On Thu, Jul 27, 2023 at 4:35 PM Le Huang @.***> wrote:

Sorry I could not get your point. Could you rephrase ur question?

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linnabrown commented 1 year ago

This file located in the temporary folder

    self.input_folder = args.input if args.input.endswith("/") else args.input +"/"
  1. You can run faa or fna. You don't need to put them at the same time.