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from __future__ import absolute_import
import unittest
from .. import SeqGroup
from .datasets import *
class Test_Coretype_SeqGroup(unittest.TestCase):
""" Tests core functionality of Alignmnets objects """
def test_fasta_parser(self):
""" test fasta read an write """
# FASTA IO
open("/tmp/ete_test_fasta.txt","w").write(fasta_example)
# Test reading from file and from string
SEQS = SeqGroup(fasta_example)
SEQS2 = SeqGroup("/tmp/ete_test_fasta.txt")
# Compare the result is the same
self.assertEqual(SEQS.write(), SEQS2.write())
# Test writing into file
SEQS.write(format="fasta", outfile="/tmp/ete_fastaIO")
self.assertEqual(SEQS.write(), fasta_example_output)
# Test SeqGroup obj integrity
self.assertEqual(SEQS.get_seq("Ago0000003"), Ago0000003)
self.assertEqual(SEQS2.get_seq("Ago0000003"), Ago0000003)
self.assertEqual(len(SEQS), len(SEQS.id2seq))
self.assertEqual("Ago0000003" in SEQS, True)
self.assertEqual("Ago" in SEQS, False)
self.assertEqual(SEQS.get_entries(), [e for e in SEQS])
# Check that the default write format is FASTA
self.assertEqual(SEQS.__str__(), SEQS.write(format="fasta"))
def test_phylip_parser(self):
""" Tests phylip read and write """
# PHYLIP INTERLEAVED
open("/tmp/ete_test_iphylip.txt","w").write(phylip_interlived)
SEQS = SeqGroup("/tmp/ete_test_iphylip.txt", format="iphylip")
SEQS2 = SeqGroup(phylip_interlived, format="iphylip")
self.assertEqual(SEQS.write(), SEQS2.write())
SEQS.write(format="iphylip", outfile="/tmp/ete_write_file")
self.assertEqual(SEQS.write(format="iphylip"), phylip_interlived)
# Test SeqGroup obj integrity
self.assertEqual(SEQS.get_seq("CYS1_DICDI"), CYS1_DICDI)
self.assertEqual(SEQS2.get_seq("CYS1_DICDI"), CYS1_DICDI)
self.assertEqual(len(SEQS), len(SEQS.id2seq))
self.assertEqual("CYS1_DICDI" in SEQS, True)
self.assertEqual(SEQS.get_entries(), [e for e in SEQS])
# PHYLIP SEQUENCIAL FORMAT
open("/tmp/ete_test_phylip.txt","w").write(phylip_sequencial)
SEQS = SeqGroup("/tmp/ete_test_phylip.txt", format="phylip")
SEQS2 = SeqGroup(phylip_sequencial, format="phylip")
self.assertEqual(SEQS.write(), SEQS2.write())
SEQS.write(format="phylip", outfile="/tmp/ete_write_file")
self.assertEqual(SEQS.write(format="phylip"), phylip_sequencial)
# Test SeqGroup obj integrity
self.assertEqual(SEQS.get_seq("CYS1_DICDI"), CYS1_DICDI)
self.assertEqual(SEQS2.get_seq("CYS1_DICDI"), CYS1_DICDI)
self.assertEqual(len(SEQS), len(SEQS.id2seq))
self.assertEqual("CYS1_DICDI" in SEQS, True)
self.assertEqual("CYS1" in SEQS, False)
self.assertEqual(SEQS.get_entries(), [e for e in SEQS])
# test write speed
#SEQS = SeqGroup()
#for i in xrange(25):
# SEQS.set_seq("seq%s" %i, "A"*500000)
#SEQS.write(outfile="/tmp/iphylip_write_test.phy", format="iphylip")
#SEQS.write(outfile="/tmp/iphylip_write_test.phy", format="phylip")
def test_alg_from_scratch(self):
alg = SeqGroup(phylip_sequencial, format="phylip")
random_seq = alg.get_seq("CATH_HUMAN")
# Add a new sequence to the alg
alg.set_seq("randomseq", random_seq.replace("A","X"))
self.assertEqual(alg.get_seq("randomseq"), random_seq.replace("A","X"))
# Exports the alignment to different formats
alg.write(format ="fasta")
alg.write(format ="iphylip")
alg.write(format ="phylip")
if __name__ == '__main__':
unittest.main()
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