class OrthoDBTest(unittest.TestCase):
def setUp(self):
self.cwd = os.path.dirname(__file__)
self.in_file = os.path.join(self.cwd, "OrthoDB", "OrthoDB6_Arthropoda_tabtext.csv")
self.my_orthodb = OrthoDB(self.in_file, 'Bombyx mori')
self.outfile = os.path.join(self.cwd, "OrthoDB", "output.txt")
def test_single_copy_genes(self):
"""We are using only part of the original OrthoDB6 file"""
genes = self.my_orthodb.single_copy_genes
self.assertEqual(len(genes), 325)
def test_copies_per_gene(self):
result = self.my_orthodb._copies_per_gene()
number_copies = result['Bombyx mori', 'BGIBMGA000894', 'EOG600001']
self.assertEqual(2, number_copies)
def test_single_copy_in_species(self):
result = self.my_orthodb._single_copy_in_species("Znev_18776")
self.assertEqual(result[0], "Zootermopsis nevadensis")
def test_copies_per_gene_table(self):
self.my_orthodb._single_copy_in_species("Znev_18776")
self.my_orthodb._copies_per_gene_table(self.outfile)
with open(self.outfile, "r") as handle:
self.assertTrue(handle.read().startswith('Genes\tZootermopsis nevadensis'))
def tearDown(self):
if os.path.isfile(self.outfile):
os.remove(self.outfile)
def setUp(self):
self.cwd = os.path.dirname(__file__)
self.in_file = os.path.join(self.cwd, "OrthoDB", "OrthoDB6_Arthropoda_tabtext.csv")
self.my_orthodb = OrthoDB(self.in_file, 'Bombyx mori')
self.outfile = os.path.join(self.cwd, "OrthoDB", "output.txt")
def test_single_copy_genes(self):
"""We are using only part of the original OrthoDB6 file"""
result = OrthoDB.single_copy_genes("OrthoDB/OrthoDB6_Arthropoda_tabtext.csv", \
"Bombyx mori")
self.assertEqual(len(result), 326)
#!/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")
def test_single_copy_in_species(self):
result = \
OrthoDB.single_copy_in_species("OrthoDB/OrthoDB6_Arthropoda_tabtext.csv", \
"Znev_18776")
self.assertEqual(result[0], "Zootermopsis nevadensis")