I am trying to run a number of BLASTs against the mouse genome - using Bioypthon to streamline things.
I would like to know how I can best do it with a remote genome (and a remote BLAST). I am aware of the NCBIWWW.qblast("blastn", "nr", fasta_string) biopthon function, whereby the seconf variable gives the database. Sadly, I was unable to find any working handle for the mouse genome.
Instead of that (or in addition to that) I would like to know how I can best do this locally. I downloaded the genbank mouse genome, and I am pretty sure the correct biopython function for this would be NcbiblastnCommandline(query, subject, outfmt=5, task="blastn"). But I have no idea how to speify my subject properly. Currently I am thinking of extracting all the files from the genbank genome (genbank/genomes/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38.p3/Primary_Assembly/assembled_chromosomes/FASTA/*.fa.gz) to .fa and iterating over them. But I hope there is a nicer way of doing this - can you help me out?
