Download fasta file from ncbi unix

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Matteo Ferla Matteo Ferla 3, 3 3 silver badges 16 16 bronze badges. Downloading a few sequences For this, you can use Entrez Direct as mentioned by dc BlueSky BlueSky 2 2 bronze badges. Whether you want a large number of files or just one file is, I guess, a personal choice. A multifasta file is fairly standard though. I don't think you can create individual files for each sequence using epost and efetch ; you will have to either use a bash script or postprocess the efetch output using the unix tool split.

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Collectives on Stack Overflow. Learn more. Downloading multiple fasta files from ncbi Ask Question. Asked 5 years, 9 months ago. Active 5 years, 9 months ago. Viewed 1k times. I'm trying to download all fasta files associated with one organism from ncbi. Any ideas on why it's rejecting these directories?

Thanks for your help. Improve this question. I'm thinking you are requesting too much too frequently on their server so they kicked you out. You should really write a shell script that sleeps inbetween each wget so you don't overload the server.

Add a comment. Active Oldest Votes. Improve this answer. Hi, thanks for your help. Unfortunately, that code still seemed to overload their server. But i'm actually trying to pull off whole genomes using the genome db rather than the nucleotide db. I think this requires the use of elink to link the id's in the genome db with the id's in the nucleotide db, which is where the data is actually stored.

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