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# Copyright 2009-2013 by Peter Cock. All rights reserved.
# Parts copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import unittest
from Bio._py3k import StringIO
from Bio import SeqIO
from Bio.SeqIO.FastaIO import FastaIterator
from Bio.Alphabet import generic_nucleotide, generic_dna
from Bio.SeqIO.FastaIO import SimpleFastaParser, FastaTwoLineParser
def title_to_ids(title):
"""Function to convert a title into the id, name, and description.
This is just a quick-n-dirty implementation, and is definetely not meant
to handle every FASTA title line case.
"""
# first split the id information from the description
# the first item is the id info block, the rest is the description
all_info = title.split(" ")
id_info = all_info[0]
rest = all_info[1:]
descr = " ".join(rest)
# now extract the ids from the id block
# gi|5690369|gb|AF158246.1|AF158246
id_info_items = id_info.split("|")
if len(id_info_items) >= 4:
assert id_info_items[2] in ["gb", "emb", "dbj", "pdb"], title
id = id_info_items[3] # the id with version info
name = id_info_items[4] # the id without version info
else:
# Fallback:
id = id_info_items[0]
name = id_info_items[0]
return id, name, descr
def read_single_with_titles(filename, alphabet):
global title_to_ids
with open(filename) as handle:
iterator = FastaIterator(handle, alphabet, title_to_ids)
record = next(iterator)
try:
second = next(iterator)
except StopIteration:
second = None
assert record is not None and second is None
return record
def read_title_and_seq(filename):
"""Crude parser that gets the first record from a FASTA file."""
with open(filename) as handle:
title = handle.readline().rstrip()
assert title.startswith(">")
seq = ""
for line in handle:
if line.startswith(">"):
break
seq += line.strip()
return title[1:], seq
class Wrapping(unittest.TestCase):
"""Tests for two-line-per-record FASTA variant."""
def test_fails(self):
self.assertRaises(ValueError, SeqIO.read, "Fasta/aster.pro", "fasta-2line")
def test_passes(self):
expected = SeqIO.read("Fasta/aster.pro", "fasta")
record = SeqIO.read("Fasta/aster_no_wrap.pro", "fasta")
self.assertEqual(expected.id, record.id)
self.assertEqual(expected.name, record.name)
self.assertEqual(expected.description, record.description)
self.assertEqual(expected.seq, record.seq)
record = SeqIO.read("Fasta/aster_no_wrap.pro", "fasta-2line")
self.assertEqual(expected.id, record.id)
self.assertEqual(expected.name, record.name)
self.assertEqual(expected.description, record.description)
self.assertEqual(expected.seq, record.seq)
class TitleFunctions(unittest.TestCase):
"""Cunning unit test where methods are added at run time."""
def simple_check(self, filename, alphabet):
"""Basic test for parsing single record FASTA files."""
title, seq = read_title_and_seq(filename) # crude parser
# First check using Bio.SeqIO.FastaIO directly with title function,
record = read_single_with_titles(filename, alphabet)
idn, name, descr = title_to_ids(title)
self.assertEqual(record.id, idn)
self.assertEqual(record.name, name)
self.assertEqual(record.description, descr)
self.assertEqual(str(record.seq), seq)
self.assertEqual(record.seq.alphabet, alphabet)
# Now check using Bio.SeqIO (default settings)
record = SeqIO.read(filename, "fasta", alphabet)
self.assertEqual(record.id, title.split()[0])
self.assertEqual(record.name, title.split()[0])
self.assertEqual(record.description, title)
self.assertEqual(str(record.seq), seq)
self.assertEqual(record.seq.alphabet, alphabet)
# Uncomment this for testing the methods are calling the right files:
# print("{%s done}" % filename)
def multi_check(self, filename, alphabet):
"""Basic test for parsing multi-record FASTA files."""
with open(filename) as handle:
re_titled = list(FastaIterator(handle, alphabet, title_to_ids))
default = list(SeqIO.parse(filename, "fasta", alphabet))
self.assertEqual(len(re_titled), len(default))
for old, new in zip(default, re_titled):
idn, name, descr = title_to_ids(old.description)
self.assertEqual(new.id, idn)
self.assertEqual(new.name, name)
self.assertEqual(new.description, descr)
self.assertEqual(str(new.seq), str(old.seq))
self.assertEqual(new.seq.alphabet, old.seq.alphabet)
# Uncomment this for testing the methods are calling the right files:
# print("{%s done}" % filename)
def test_no_name(self):
"""Test FASTA record with no identifier."""
handle = StringIO(">\nACGT")
record = SeqIO.read(handle, "fasta")
handle.close()
self.assertEqual(str(record.seq), "ACGT")
self.assertEqual("", record.id)
self.assertEqual("", record.name)
self.assertEqual("", record.description)
class TestSimpleFastaParsers(unittest.TestCase):
"""Test SimpleFastaParser and FastaTwoLineParser directly."""
# Regular cases input strings and outputs
ins_two_line = [">1\nACGT", ">1\nACGT",
">1\nACGT\n>2\nACGT"]
outs_two_line = [[("1", "ACGT")], [("1", "ACGT")],
[("1", "ACGT"), ("2", "ACGT")]]
ins_multiline = [">1\nACGT\nACGT",
">1\nACGT\nACGT\n>2\nACGT\nACGT"]
outs_multiline = [[("1", "ACGTACGT")],
[("1", "ACGTACGT"), ("2", "ACGTACGT")]]
# Edge case input strings and outputs
ins_two_line_edges = [">\nACGT", ">1\n\n",
">1>1\n\n>1\n\n", ""]
outs_two_line_edges = [[("", "ACGT")], [("1", "")],
[("1>1", ""), ("1", "")], []]
ins_simple_edges = [">1", ">1\n\n\n",
">\n>1\n>2"]
outs_simple_edges = [[("1", "")], [("1", "")],
[("", ""), ("1", ""), ("2", "")]]
def test_regular_SimpleFastaParser(self):
""""Test regular SimpleFastaParser cases."""
for inp, out in zip(self.ins_two_line, self.outs_two_line):
handle1 = StringIO(inp)
handle2 = StringIO(inp + '\n')
self.assertEqual(list(SimpleFastaParser(handle1)), out)
self.assertEqual(list(SimpleFastaParser(handle2)), out)
for inp, out in zip(self.ins_multiline, self.outs_multiline):
handle1 = StringIO(inp)
handle2 = StringIO(inp + '\n')
self.assertEqual(list(SimpleFastaParser(handle1)), out)
self.assertEqual(list(SimpleFastaParser(handle2)), out)
def test_regular_FastaTwoLineParser(self):
"""Test regular FastaTwoLineParser cases."""
for inp, out in zip(self.ins_two_line, self.outs_two_line):
handle1 = StringIO(inp)
handle2 = StringIO(inp + '\n')
self.assertEqual(list(FastaTwoLineParser(handle1)), out)
self.assertEqual(list(FastaTwoLineParser(handle2)), out)
def test_edgecases_SimpleFastaParser(self):
"""Test SimpleFastaParser edge-cases."""
for inp, out in zip(self.ins_two_line_edges, self.outs_two_line_edges):
handle = StringIO(inp)
self.assertEqual(list(SimpleFastaParser(handle)), out)
for inp, out in zip(self.ins_simple_edges, self.outs_simple_edges):
handle = StringIO(inp)
self.assertEqual(list(SimpleFastaParser(handle)), out)
def test_edgecases_FastaTwoLineParser(self):
"""Test FastaTwoLineParser edge-cases."""
for inp, out in zip(self.ins_two_line_edges, self.outs_two_line_edges):
handle = StringIO(inp)
self.assertEqual(list(FastaTwoLineParser(handle)), out)
def test_exceptions_FastaTwoLineParser(self):
"""Test FastaTwoLineParser exceptions."""
for inp in self.ins_multiline + self.ins_simple_edges:
handle = StringIO(inp)
with self.assertRaises(ValueError):
list(FastaTwoLineParser(handle))
single_nucleic_files = ['Fasta/lupine.nu', 'Fasta/elderberry.nu',
'Fasta/phlox.nu', 'Fasta/centaurea.nu',
'Fasta/wisteria.nu', 'Fasta/sweetpea.nu',
'Fasta/lavender.nu', 'Fasta/f001']
multi_dna_files = ['Quality/example.fasta']
single_amino_files = ['Fasta/aster.pro', 'Fasta/rosemary.pro',
'Fasta/rose.pro', 'Fasta/loveliesbleeding.pro']
multi_amino_files = ['Fasta/f002', 'Fasta/fa01']
for filename in single_nucleic_files:
name = filename.split(".")[0]
def funct(fn):
f = lambda x: x.simple_check(fn, generic_nucleotide)
f.__doc__ = "Checking nucleotide file %s" % fn
return f
setattr(TitleFunctions, "test_nuc_%s" % name, funct(filename))
del funct
for filename in multi_dna_files:
name = filename.split(".")[0]
def funct(fn):
f = lambda x: x.multi_check(fn, generic_dna)
f.__doc__ = "Checking multi DNA file %s" % fn
return f
setattr(TitleFunctions, "test_mutli_dna_%s" % name, funct(filename))
del funct
for filename in single_amino_files:
name = filename.split(".")[0]
def funct(fn):
f = lambda x: x.simple_check(fn, generic_nucleotide)
f.__doc__ = "Checking protein file %s" % fn
return f
setattr(TitleFunctions, "test_pro_%s" % name, funct(filename))
del funct
for filename in multi_amino_files:
name = filename.split(".")[0]
def funct(fn):
f = lambda x: x.multi_check(fn, generic_dna)
f.__doc__ = "Checking multi protein file %s" % fn
return f
setattr(TitleFunctions, "test_mutli_pro_%s" % name, funct(filename))
del funct
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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