In task1-files, there is a text file of different species names. Write a general program that takes this list as input (using argparse), gets the taxonomic information from NCBI for each sample, and writes that to a new file as output (again, get the output file name using argparse). Format the output file as a CSV. The output file should contain the values for each species for the following: superclass, class, subclass, infraclass, superorder, order, superfamily, family, and genus. Be sure that your program is formatted correctly (PEP8) and be sure that your file works appropriately with any generic list of species. Also be sure that you pass your email to NCBI (Entrez.email) and that you limit your requests to 1 per second.

Loxosceles reclusa is also known as the "brown recluse", a spider that is known to occasionally bite humans and the bites of which cause severe tissue necrosis around the site of the bite. Write a program that queries GenBank for all the sequence data for this spider and then writes the sequence data to a file in FASTA format. Use argparse to take the name of the organism as input and the name of some FASTA file as output. Be sure that your program is formatted correctly (PEP8). Also be sure that you pass your email to NCBI (Entrez.email) and that you limit your requests to 1 per second.

Building on Task 2, modify your program above to get GI record of each sequence from NCBI (e.g. do not work from the FASTA file you created) and the send those records to NCBI BLAST to perform a blastn search of each sequence against the nt (nucleotide) database. Write each BLAST result (the result for each sequence, which may consist of several hits) out to text files in BLAST format (use argparse to get the output directory name from the user). We didn't cover BLAST searches in class, so you'll need to look at the BioPython Cookbook and go from there. Be sure that your program is formatted correctly (PEP8). Also be sure that you pass your email to NCBI (Entrez.email) and that you limit your requests to 1 per second.