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#!/usr/bin/python
# -*- coding: utf-8 -*-
from gt.core.encseq import *
from gt.core.error import GTError
from gt.core import readmode
import unittest
import tempfile
import sys
import os
import string
class EncodedsequenceTest(unittest.TestCase):
def setUp(self):
self.dnaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False)
self.dnaseqfile.close()
self.dnafname = self.dnaseqfile.name
self.dnafile = open(self.dnafname, "w")
self.dseq1 = "agtccagctgtcagctagcgggcccgatgatatttt"
self.dseq2 = "gtgctgtac"
self.dseq3 = "gtacagcac"
self.dseq4 = "aaaatatcatcgggcccgctagctgacagctggact"
self.dnafile.write(">seq1\n" + self.dseq1 + "\n")
self.dnafile.write(">seq2\n" + self.dseq2 + "\n")
self.aaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False)
self.aaseqfile.close()
self.aafname = self.aaseqfile.name
self.aafile = open(self.aafname, "w")
self.aaseq1 = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG"
self.aaseq2 = "KMNAVE"
self.aafile.write(">seq1\n" + self.aaseq1 + "\n")
self.aafile.write(">seq2\n" + self.aaseq2 + "\n")
self.dnafile.close()
self.aafile.close()
self.idxsuffixes = ['esq', 'des', 'ssp', 'sds']
def tearDown(self):
pass # os.unlink(self.dnafname)
# os.unlink(self.aafname)
def create_es(self, indexname):
ee = EncseqEncoder()
return ee.encode([self.dnafname], indexname)
def create_es_protein(self, indexname):
ee = EncseqEncoder()
return ee.encode([self.aafname], indexname)
def create_mem(self):
a = Alphabet.create_dna()
eb = EncseqBuilder(a)
eb.enable_description_support()
eb.enable_multiseq_support()
eb.add_string(self.dseq1, 'seq1')
eb.add_string(self.dseq2, 'seq2')
return eb.build()
def create_mem_protein(self):
a = Alphabet.create_protein()
eb = EncseqBuilder(a)
eb.enable_description_support()
eb.enable_multiseq_support()
eb.add_string(self.aaseq1, 'seq1')
eb.add_string(self.aaseq2, 'seq2')
return eb.build()
def delete_idx(self, indexname):
for suf in self.idxsuffixes:
if os.path.isfile(indexname + "." + suf):
os.unlink(indexname + "." + suf)
def test_create_new(self):
val = self.create_es("foo")
for suf in self.idxsuffixes:
self.assertTrue(os.path.isfile("foo." + suf))
self.delete_idx("foo")
def test_create_mapped(self):
self.create_es("foo_mapped")
el = EncseqLoader()
es = el.load("foo_mapped")
self.assertNotEqual(es, None)
self.delete_idx("foo_mapped")
def test_map_fail(self):
el = EncseqLoader()
self.assertRaises(IOError, el.load, "foo_fail")
def test_dna(self):
self.create_es("foo")
el = EncseqLoader()
es = el.load("foo")
self.run_test_descriptions(es)
self.run_test_get_encoded_char(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_num_seqs(es)
self.run_test_num_files(es)
self.run_test_seq_length(es)
self.run_test_seq_startpos(es)
self.run_test_seq_substr_encoded(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_seq_substr_plain(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_seq_substr_sequential(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_total_length(es)
self.delete_idx("foo")
es = self.create_mem()
self.run_test_descriptions(es)
self.run_test_get_encoded_char(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_num_seqs(es)
self.run_test_num_files_mem(es)
self.run_test_seq_length(es)
self.run_test_seq_substr_encoded(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_seq_substr_plain(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_seq_substr_sequential(
es, self.dseq1, self.dseq2, self.dseq3, self.dseq4)
self.run_test_total_length(es)
def test_protein(self):
self.create_es_protein("foo")
el = EncseqLoader()
es = el.load("foo")
self.run_test_descriptions(es)
self.run_test_get_encoded_char(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_num_seqs(es)
self.run_test_num_files(es)
self.run_test_seq_startpos_protein(es)
self.run_test_seq_length_protein(es)
self.run_test_file_length_protein(es)
self.run_test_seq_substr_encoded(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_seq_substr_plain(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_seq_substr_sequential(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_total_length_protein(es)
self.delete_idx("foo")
es = self.create_mem_protein()
self.run_test_descriptions(es)
self.run_test_get_encoded_char(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_num_seqs(es)
self.run_test_num_files_mem(es)
self.run_test_seq_length_protein(es)
self.run_test_seq_substr_encoded(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_seq_substr_plain(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_seq_substr_sequential(
es, self.aaseq1, self.aaseq2, None, None)
self.run_test_total_length_protein(es)
def run_test_num_seqs(self, es):
self.assertEqual(es.num_of_sequences(), 2)
if es.alphabet().is_dna():
es.mirror()
self.assertEqual(es.num_of_sequences(), 4)
es.unmirror()
def run_test_num_files(self, es):
self.assertEqual(es.num_of_files(), 1)
if es.alphabet().is_dna():
es.mirror()
self.assertEqual(es.num_of_files(), 1)
es.unmirror()
def run_test_num_files_mem(self, es):
self.assertEqual(es.num_of_files(), 1)
if es.alphabet().is_dna():
es.mirror()
self.assertEqual(es.num_of_files(), 1)
es.unmirror()
def run_test_descriptions(self, es):
self.assertRaises(GTError, es.description, 2)
self.assertEqual(es.description(0), "seq1")
self.assertEqual(es.description(1), "seq2")
if es.alphabet().is_dna():
es.mirror()
self.assertRaises(GTError, es.description, 5)
self.assertEqual(es.description(2), "seq2")
self.assertEqual(es.description(3), "seq1")
es.unmirror()
def run_test_total_length(self, es):
self.assertEqual(es.total_length(), 46)
if es.alphabet().is_dna():
es.mirror()
self.assertEqual(es.total_length(), 93)
es.unmirror()
def run_test_total_length_protein(self, es):
self.assertEqual(es.total_length(), 37)
def run_test_get_encoded_char(self, es, seq1, seq2, seq3, seq4):
a = es.alphabet()
for i, c in enumerate(seq1):
encchar = es.get_encoded_char(i, readmode.FORWARD)
self.assertEqual(a.decode(encchar), c)
for i, c in enumerate(seq2[::-1]):
encchar = es.get_encoded_char(i, readmode.REVERSE)
self.assertEqual(a.decode(encchar), c)
if es.alphabet().is_dna():
es.mirror()
for i, c in enumerate(seq3):
encchar = es.get_encoded_char(47 + i, readmode.FORWARD)
self.assertEqual(a.decode(encchar), c)
for i, c in enumerate(seq4[::-1]):
encchar = es.get_encoded_char(i, readmode.REVERSE)
self.assertEqual(a.decode(encchar), c)
es.unmirror()
def run_test_seq_startpos(self, es):
self.assertEqual(es.seqstartpos(0), 0)
self.assertEqual(es.seqstartpos(1), 37)
def run_test_seq_startpos_protein(self, es):
self.assertEqual(es.seqstartpos(0), 0)
self.assertEqual(es.seqstartpos(1), 31)
def run_test_seq_length(self, es):
self.assertEqual(es.seqlength(0), 36)
self.assertEqual(es.seqlength(1), 9)
def run_test_file_length(self, es):
self.assertEqual(es.effective_filelength(0), 46)
def run_test_seq_length_protein(self, es):
self.assertEqual(es.seqlength(0), 30)
self.assertEqual(es.seqlength(1), 6)
def run_test_file_length_protein(self, es):
self.assertEqual(es.effective_filelength(0), 37)
def run_test_seq_substr_encoded(self, es, seq1, seq2, seq3, seq4):
start = 3
end = 13
res = es.extract_encoded(start, end)
a = es.alphabet()
for i in range(start, end):
self.assertEqual(a.decode(res[i - start]), seq1[i])
start = 0
end = 5
ssp = es.seqstartpos(1)
res = es.extract_encoded(ssp + start, ssp + end)
for i in range(start, end):
self.assertEqual(a.decode(res[i - start]), seq2[i])
if es.alphabet().is_dna():
es.mirror()
start = 3
end = 8
ssp = es.seqstartpos(2)
res = es.extract_encoded(ssp + start, ssp + end)
for i in range(start, end):
self.assertEqual(a.decode(res[i - start]), seq3[i])
start = 0
end = 5
ssp = es.seqstartpos(3)
res = es.extract_encoded(ssp + start, ssp + end)
for i in range(start, end):
self.assertEqual(a.decode(res[i - start]), seq4[i])
es.unmirror()
def run_test_seq_substr_plain(self, es, seq1, seq2, seq3, seq4):
start = 3
end = 13
self.assertEqual(es.extract_decoded(start, end), seq1[start:end + 1])
start = 0
end = 5
ssp = es.seqstartpos(1)
self.assertEqual(es.extract_decoded(ssp + start, ssp + end),
seq2[start:end + 1])
if es.alphabet().is_dna():
es.mirror()
start = 3
end = 8
ssp = es.seqstartpos(2)
res = es.extract_encoded(ssp + start, ssp + end)
for i in range(start, end):
self.assertEqual(es.extract_decoded(ssp + start, ssp + end),
seq3[start:end + 1])
start = 0
end = 5
ssp = es.seqstartpos(3)
res = es.extract_encoded(ssp + start, ssp + end)
for i in range(start, end):
self.assertEqual(es.extract_decoded(ssp + start, ssp + end),
seq4[start:end + 1])
es.unmirror()
def run_test_seq_substr_sequential(self, es, seq1, seq2, seq3, seq4):
start = 3
end = 13
er = es.create_reader_with_readmode(readmode.FORWARD, start)
a = es.alphabet()
for i in range(start, end):
self.assertEqual(a.decode(er.next_encoded_char()), seq1[i])
start = es.seqstartpos(1)
end = start + 5
er = es.create_reader_with_readmode(readmode.FORWARD, start)
for i in range(start - start, end - start):
self.assertEqual(a.decode(er.next_encoded_char()), seq2[i])
if es.alphabet().is_dna():
es.mirror()
start = es.seqstartpos(2)
end = start + 5
er = es.create_reader_with_readmode(readmode.FORWARD, start)
for i in range(start - start, end - start):
self.assertEqual(a.decode(er.next_encoded_char()), seq3[i])
start = es.seqstartpos(3)
end = start + 5
er = es.create_reader_with_readmode(readmode.FORWARD, start)
for i in range(start - start, end - start):
self.assertEqual(a.decode(er.next_encoded_char()), seq4[i])
es.unmirror()
if __name__ == "__main__":
unittest.main()
|
