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#!/usr/bin/env python
"""Tests for FASTA sequence format writer.
"""
from cogent.util.unit_test import TestCase, main
from cogent.format.fasta import fasta_from_sequences, fasta_from_alignment
from cogent.core.alignment import Alignment
from cogent.core.sequence import Sequence
from cogent.core.info import Info
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Gavin Huttley", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Production"
class FastaTests(TestCase):
"""Tests for Fasta writer.
"""
def setUp(self):
"""Setup for Fasta tests."""
self.strings = ['AAAA','CCCC','gggg','uuuu']
self.labels = ['1st','2nd','3rd','4th']
self.infos = ["Dog", "Cat", "Mouse", "Rat"]
self.sequences_with_labels = map(Sequence, self.strings)
self.sequences_with_names = map(Sequence, self.strings)
for l,sl,sn in zip(self.labels,self.sequences_with_labels,\
self.sequences_with_names):
sl.Label = l
sn.Name = l
self.fasta_no_label='>0\nAAAA\n>1\nCCCC\n>2\ngggg\n>3\nuuuu'
self.fasta_with_label=\
'>1st\nAAAA\n>2nd\nCCCC\n>3rd\nGGGG\n>4th\nUUUU'
self.fasta_with_label_lw2=\
'>1st\nAA\nAA\n>2nd\nCC\nCC\n>3rd\nGG\nGG\n>4th\nUU\nUU'
self.alignment_dict = {'1st':'AAAA','2nd':'CCCC','3rd':'GGGG',
'4th':'UUUU'}
self.alignment_object = Alignment(self.alignment_dict)
for label, info in zip(self.labels, self.infos):
self.alignment_object.NamedSeqs[label].Info = Info(species=info)
self.fasta_with_label_species=\
'>1st:Dog\nAAAA\n>2nd:Cat\nCCCC\n>3rd:Mouse\nGGGG\n>4th:Rat\nUUUU'
self.alignment_object.RowOrder = ['1st','2nd','3rd','4th']
def test_fastaFromSequence(self):
"""should return correct fasta string."""
self.assertEqual(fasta_from_sequences(''),'')
self.assertEqual(fasta_from_sequences(self.strings),\
self.fasta_no_label)
self.assertEqual(fasta_from_sequences(self.sequences_with_labels),\
self.fasta_with_label)
self.assertEqual(fasta_from_sequences(self.sequences_with_names),\
self.fasta_with_label)
make_seqlabel = lambda seq: "%s:%s" % (seq.Name, seq.Info.species)
seqs = [self.alignment_object.NamedSeqs[label] for label in self.labels]
self.assertEqual(fasta_from_sequences(seqs,
make_seqlabel=make_seqlabel), self.fasta_with_label_species)
def test_fasta_from_alignment(self):
"""should return correct fasta string."""
self.assertEqual(fasta_from_alignment({}),'')
self.assertEqual(fasta_from_alignment(self.alignment_dict),\
self.fasta_with_label)
self.assertEqual(fasta_from_alignment(self.alignment_dict,
line_wrap=2),self.fasta_with_label_lw2)
self.assertEqual(fasta_from_alignment(self.alignment_object),\
self.fasta_with_label)
if __name__ == "__main__":
main()
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