# 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. """Tests for Bio.SeqIO.FastaIO module.""" import unittest from io import StringIO from Bio import SeqIO from Bio.SeqIO.FastaIO import FastaTwoLineParser from Bio.SeqIO.FastaIO import SimpleFastaParser from Bio import BiopythonDeprecationWarning def title_to_ids(title): """Convert a FASTA title line into the id, name, and description. This is just a quick-n-dirty implementation, and is definitely 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_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): """Test case which should fail.""" self.assertRaises(ValueError, SeqIO.read, "Fasta/aster.pro", "fasta-2line") def test_passes(self): """Test case which should pass.""" 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): """Test using title functions.""" def simple_check(self, filename): """Test parsing single record FASTA files.""" msg = f"Test failure parsing file {filename}" title, seq = read_title_and_seq(filename) # crude parser record = SeqIO.read(filename, "fasta") self.assertEqual(record.id, title.split()[0], msg=msg) self.assertEqual(record.name, title.split()[0], msg=msg) self.assertEqual(record.description, title, msg=msg) self.assertEqual(record.seq, seq, msg=msg) # 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(record.seq, "ACGT") self.assertEqual("", record.id) self.assertEqual("", record.name) self.assertEqual("", record.description) def test_single_nucleic_files(self): """Test Fasta files containing a single nucleotide sequence.""" paths = ( "Fasta/lupine.nu", "Fasta/elderberry.nu", "Fasta/phlox.nu", "Fasta/centaurea.nu", "Fasta/wisteria.nu", "Fasta/sweetpea.nu", "Fasta/lavender.nu", "Fasta/f001", ) for path in paths: self.simple_check(path) def test_single_proteino_files(self): """Test Fasta files containing a single protein sequence.""" paths = ( "Fasta/aster.pro", "Fasta/rosemary.pro", "Fasta/rose.pro", "Fasta/loveliesbleeding.pro", ) for path in paths: self.simple_check(path) 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)) class TestFastaWithComments(unittest.TestCase): """Test FastaBlastIterator and FastaPearsonIterator.""" expected = SeqIO.read("Fasta/aster.pro", "fasta") def test_fasta_blast(self): """Test FastaBlastIterator.""" expected = self.expected record = SeqIO.read("Fasta/aster_blast.pro", "fasta-blast") self.assertEqual(expected.id, record.id) self.assertEqual(expected.name, record.name) self.assertEqual(expected.description, record.description) self.assertEqual(expected.seq, record.seq) def test_fasta_pearson(self): """Test FastaPearsonIterator.""" expected = self.expected record = SeqIO.read("Fasta/aster_pearson.pro", "fasta-pearson") self.assertEqual(expected.id, record.id) self.assertEqual(expected.name, record.name) self.assertEqual(expected.description, record.description) self.assertEqual(expected.seq, record.seq) def test_valueerrors(self): """Test if ValueErrors are raised if comments are found unexpectedly.""" self.assertRaises( ValueError, SeqIO.read, "Fasta/aster_pearson.pro", "fasta-blast" ) with self.assertWarns(BiopythonDeprecationWarning): record = SeqIO.read("Fasta/aster_pearson.pro", "fasta") with self.assertWarns(BiopythonDeprecationWarning): record = SeqIO.read("Fasta/aster_blast.pro", "fasta") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)