Is there a way to download individual mitochondrial sequences from NCBI without having to scrape from their webpages or to download thousands of other sequences alongside. Is there some programmatic way to access these fasta data, for example:
https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1?report=fasta
Following this post:
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_012920.1&rettype=fasta&retmode=text" >mtDNA.fa
You can use "Send to" drop down on that page to send the data to a file. No scraping needed.
If you have many of these to get then using NCBI eUtils is the best option. For example for the link you posted you can do this
efetch -db nuccore -id NC_012920.1 -format fasta > NC_012920.fa
Thanks, but installing eutils as below failed with errors: "Is libxml2 installed?" (yes, it is...)
pip3 install eutils
Glad you mentioned eutils though, as it led me to find this post, which showed me how to build the URL in the answer below.
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