Find location of genes in reference sequences

[dkoslicki]

The following will help with that task:

NCBI FTP site: ftp.ncbi.nlm.nih.gov (username: anonymous, pw: your email)
location /gene/DATA has a file gene2refseq that lists all the known genes, their corresponding locations and the accessions for the genomes that they belong to.

Pull out specific regions of a genome:

wget "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NZ_CP096169.1&strand=1&rettype=fasta&seq_start=0&seq_stop=1385&retmode=text" -O out.fa

Idea:

1. Select a bunch of accessions for which we have gene information (from the gene2refseq)
2. Download their corresponding whole genomes
3. Create a mapping file that maps regions to genes (slight modification of gene2refseq)
4. Download the genes themselves for training of sourmash and Diamond
5. Create a file that takes a bbmap simulation and spits out the genes covered in the simulation, as well as the %bp of the gene covered and the mean/median/summary of the total amount of bp mapped to each gene

[dkoslicki]

This will pull the amino acid sequence itself

wget "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NZ_CP096169.1&strand=1&rettype=fasta_cds_aa&seq_start=0&seq_stop=1385&retmode=text" -O out.fa