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.
Peter Menzel Peter Menzel 4 4 silver badges 9 9 bronze badges. Command-line method using EDirect This method uses Entrez Direct to first query the Assembly database for all available genomes, parses the output to extract the ftp path and downloads data using wget command.
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Bioinformatics Stack Exchange works best with JavaScript enabled. Accept all cookies Customize settings. However, Mick'sscripts are written in Perl specific to actually building a Kraken database as advertised. Use the text query to retrieve the records from the appropriate Entrez database. If desired, change the display format using the Display pulldown menu. Choose File from the 'Send to' menu, then select the desired format and click 'Create File.
Alternatively, ncbi-genome-download is packaged in conda. At the moment, this means versions 2. Specifically, no attempt at testing under Python versions older than 2. If your system is stuck on an older version of Python, consider using a tool likeHomebrew or Linuxbrew to obtain a more up-to-dateversion.
If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:. It is possible to download multiple formats by supplying a list of formats or simply download all formats:. Note : The quotes are important. Again, this is a simple string match on the organismname provided by the NCBI. Then, pass the path to that file e. You can make the string match fuzzy using the --fuzzy-genus option.
This can be handy if you need to matcha value in the middle of the NCBI organism name, like so:. Note : The above command will download all bacterial genomes containing 'coelicolor' anywhere in theirorganism name from RefSeq. Note : The above command will download all RefSeq genomes belonging to Escherichia coli.
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