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# !/usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Tests for general FASTA reading.
"""
import unittest
import dendropy
from dendropy.test.support import dendropytest
from dendropy.test.support import pathmap
from dendropy.test.support import standard_file_test_chars
class FastaDnaReaderTestCase(
standard_file_test_chars.DnaTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_fasta(self):
src_path = pathmap.char_source_path("standard-test-chars-dna.fasta")
self.verify_get_from(
matrix_type=dendropy.DnaCharacterMatrix,
src_filepath=src_path,
schema="fasta",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class FastaRnaReaderTestCase(
standard_file_test_chars.RnaTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_fasta(self):
src_path = pathmap.char_source_path("standard-test-chars-rna.fasta")
self.verify_get_from(
matrix_type=dendropy.RnaCharacterMatrix,
src_filepath=src_path,
schema="fasta",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
class FastaProteinReaderTestCase(
standard_file_test_chars.ProteinTestChecker,
dendropytest.ExtendedTestCase):
@classmethod
def setUpClass(cls):
cls.build()
def test_basic_fasta(self):
src_path = pathmap.char_source_path("standard-test-chars-protein.fasta")
self.verify_get_from(
matrix_type=dendropy.ProteinCharacterMatrix,
src_filepath=src_path,
schema="fasta",
factory_kwargs={},
check_taxon_annotations=False,
check_matrix_annotations=False,
check_sequence_annotations=False,
check_column_annotations=False,
check_cell_annotations=False)
if __name__ == "__main__":
unittest.main()
|
