def test_get_cds(self):
"""Extracting genes and saving them as fasta file"""
BLAST.get_cds(self.genes, self.genome)
f = open("pulled_seqs.fasta", "r")
result = len(f.read())
f.close()
self.assertEqual(result, 54397)
os.remove("pulled_seqs.fasta")
#!/usr/bin/env python
import os;
from pyphylogenomics import OrthoDB
from pyphylogenomics import BLAST
"""
We will find all single-copy genes for the silk moth Bombyx mori using the table
from OrthoDB as input file:
"""
in_file = 'data/OrthoDB6_Arthropoda_tabtext.csv'
genes = OrthoDB.single_copy_genes(in_file, 'Bombyx mori')
"""
Pull all sequences for our gene IDs from the CDS file and write them to a file
pulled_seqs.fa:
"""
cds_file = "data/silkcds.fa"
if os.path.exists("data/pulled_seqs.fasta") != True:
BLAST.get_cds(genes, cds_file)
print "File moved to data/pulled_seqs.fa"
os.rename("pulled_seqs.fasta", "data/pulled_seqs.fasta")
