Set-up & Binder components for Python Lesson 5
Accessing data from NCBI can sometimes be a pain in the a**. One common problem I run into is downloading genomes from GenBank in a large-scale automated fashion.
(Almost) Daily NCBI produces an update of the current genomes in GenBank. You can download that content through their FTP website.
The file assembly_summary_genbank.txt contains identifiers and the FTP address for all genomes in GenBank. For the version I am currently looking at consists of file that is 212MB and contains 722,260 genome entries.
If we had a list of unique identifiers linked to genomes we were interested in, we could create a file that has the FTP locations of all the files we are interested in, and download them using the Unix command wget.
Provided a list of unique identifiers, create wget commands to download the genome files of interest.
The file assembly_summary_genbank_subset.txt contains 15 entries to practice parsing with - sag-uniq-ids.txt & taxon-ids.txt provide two different types of unique identifiers that can be parsed from this list.