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pmenzel / download-refseq-genomes

Perl script to download genomes within a clade from NCBI Refseq
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download from a list of taxid? #2

Open ganiatgithub opened 5 years ago

ganiatgithub commented 5 years ago

Hey,

Thank you for the cool script. I followed from here: https://bioinformatics.stackexchange.com/questions/4976/how-to-automate-ncbi-genome-download

Now I have a list of taxid, say in a .txt file, each line contains a taxid Can this perl script take the .txt file and download all the corresponding genomes?

Many thanks!

pmenzel commented 5 years ago

Hi, this feature is missing so far, the script only accepts one taxon id per run. A quick solution would be smth like this:

cat idlist.txt | xargs -n 1 ./download-refseq-genomes.pl
ganiatgithub commented 5 years ago

Thank you very much, really appreciate it!