"""Testing facility for conkit.io.FastaIO"""
__author__ = "Felix Simkovic"
__date__ = "09 Sep 2016"
import os
import unittest
from conkit.io.fasta import FastaParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestFastaParser(ParserTestCase):
[docs] def test_read_1(self):
seq = """>00FAF_A <unknown description>
GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLK
EVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKAVSGAIVAQRGPGRSA
SSEHP
"""
f_name = self.tempfile(content=seq)
parser = FastaParser()
with open(f_name, "r") as f_in:
sequence_file = parser.read(f_in)
sequence_entry = sequence_file.top_sequence
ref_id = "00FAF_A <unknown description>"
self.assertEqual(ref_id, sequence_entry.id)
ref_seq = "GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLKEVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKAVSGAIVAQRGPGRSASSEHP"
self.assertEqual(ref_seq, sequence_entry.seq)
[docs] def test_read_2(self):
seq = """# Hello World
>00FAF_A <unknown description>
GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLK
"""
f_name = self.tempfile(content=seq)
parser = FastaParser()
with open(f_name, "r") as f_in:
sequence_file = parser.read(f_in)
sequence_entry = sequence_file.top_sequence
ref_f_remark = [" Hello World"]
self.assertEqual(ref_f_remark, sequence_file.remark)
ref_id = "00FAF_A <unknown description>"
self.assertEqual(ref_id, sequence_entry.id)
ref_seq = "GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLK"
self.assertEqual(ref_seq, sequence_entry.seq)
[docs] def test_read_3(self):
msa = """#foo
#bar
>seq1
GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYF
>seq2
EVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKA
>seq3
EVHKVQECKQSDIMMRDNLFEIVTTSRTFWKRRYFQLDENTIGYF
"""
f_name = self.tempfile(content=msa)
parser = FastaParser()
with open(f_name, "r") as f_in:
sequence_file = parser.read(f_in)
self.assertEqual(["foo", "bar"], sequence_file.remark)
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual("seq1", sequence_entry.id)
self.assertEqual("GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYF", sequence_entry.seq)
elif i == 1:
self.assertEqual("seq2", sequence_entry.id)
self.assertEqual("EVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKA", sequence_entry.seq)
elif i == 2:
self.assertEqual("seq3", sequence_entry.id)
self.assertEqual("EVHKVQECKQSDIMMRDNLFEIVTTSRTFWKRRYFQLDENTIGYF", sequence_entry.seq)
[docs] def test_write_1(self):
seq = [
">00FAF_A|<unknown description>",
"GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLK",
"EVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKAVSGAIVAQRGPGRSA",
"SSEHP",
]
f_name_in = self.tempfile(content="\n".join(seq))
f_name_out = self.tempfile()
parser = FastaParser()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
sequence_file = parser.read(f_in)
parser.write(f_out, sequence_file)
with open(f_name_out, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(seq, output)
[docs] def test_write_2(self):
seq = [
"# Hello World",
">00FAF_A|<unknown description>",
"GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLK",
]
f_name_in = self.tempfile(content="\n".join(seq))
f_name_out = self.tempfile()
parser = FastaParser()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
sequence_file = parser.read(f_in)
parser.write(f_out, sequence_file)
with open(f_name_out, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(seq, output)
[docs] def test_write_3(self):
msa = [
"#foo",
"#bar",
">seq1",
"GSMFTPKPPQDSAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYF",
">seq2",
"EVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKA",
">seq3",
"EVHKVQECKQSDIMMRDNLFEIVTTSRTFWKRRYFQLDENTIGYF",
]
f_name_in = self.tempfile(content="\n".join(msa))
f_name_out = self.tempfile()
parser = FastaParser()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
sequence_file = parser.read(f_in)
parser.write(f_out, sequence_file)
with open(f_name_out, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(msa, output)
if __name__ == "__main__":
unittest.main(verbosity=2)
