#!/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, os import string class EncodedsequenceTest(unittest.TestCase): def setUp(self): self.dnaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False) self.dseq1 = "agtccagctgtcagctagcgggcccgatgatatttt" self.dseq2 = "gtgctgtac" self.dseq3 = "gtacagcac" self.dseq4 = "aaaatatcatcgggcccgctagctgacagctggact" self.dnaseqfile.write(">seq1\n"+self.dseq1+"\n") self.dnaseqfile.write(">seq2\n"+self.dseq2+"\n") self.aaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False) self.aaseq1 = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG" self.aaseq2 = "KMNAVE" self.aaseqfile.write(">seq1\n"+self.aaseq1+"\n") self.aaseqfile.write(">seq2\n"+self.aaseq2+"\n") self.dnaseqfile.close() self.aaseqfile.close() self.idxsuffixes = ['esq','des','ssp','sds'] def tearDown(self): os.unlink(self.dnaseqfile.name) os.unlink(self.aaseqfile.name) def create_es(self, indexname): ee = EncseqEncoder() return ee.encode([self.dnaseqfile.name], indexname) def create_es_protein(self, indexname): ee = EncseqEncoder() return ee.encode([self.aaseqfile.name], 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: 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.assertEquals(es.num_of_sequences(), 2) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.num_of_sequences(), 4) es.unmirror() def run_test_num_files(self, es): self.assertEquals(es.num_of_files(), 1) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.num_of_files(), 1) es.unmirror() def run_test_num_files_mem(self, es): self.assertEquals(es.num_of_files(), 1) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.num_of_files(), 1) es.unmirror() def run_test_descriptions(self, es): self.assertRaises(GTError, es.description, 2) self.assertEquals(es.description(0), "seq1") self.assertEquals(es.description(1), "seq2") if es.alphabet().is_dna(): es.mirror() self.assertRaises(GTError, es.description, 5) self.assertEquals(es.description(2), "seq2") self.assertEquals(es.description(3), "seq1") es.unmirror() def run_test_total_length(self, es): self.assertEquals(es.total_length(), 46) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.total_length(), 93) es.unmirror() def run_test_total_length_protein(self, es): self.assertEquals(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.assertEquals(a.decode(encchar), c) for i, c in enumerate(seq2[::-1]): encchar = es.get_encoded_char(i, readmode.REVERSE) self.assertEquals(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.assertEquals(a.decode(encchar), c) for i, c in enumerate(seq4[::-1]): encchar = es.get_encoded_char(i, readmode.REVERSE) self.assertEquals(a.decode(encchar), c) es.unmirror() def run_test_seq_startpos(self, es): self.assertEquals(es.seqstartpos(0), 0) self.assertEquals(es.seqstartpos(1), 37) def run_test_seq_startpos_protein(self, es): self.assertEquals(es.seqstartpos(0), 0) self.assertEquals(es.seqstartpos(1), 31) def run_test_seq_length(self, es): self.assertEquals(es.seqlength(0), 36) self.assertEquals(es.seqlength(1), 9) def run_test_file_length(self, es): self.assertEquals(es.effective_filelength(0), 46) def run_test_seq_length_protein(self, es): self.assertEquals(es.seqlength(0), 30) self.assertEquals(es.seqlength(1), 6) def run_test_file_length_protein(self, es): self.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(es.extract_decoded(start, end), seq1[start:end+1]) start = 0 end = 5 ssp = es.seqstartpos(1) self.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(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.assertEquals(a.decode(er.next_encoded_char()), seq4[i]) es.unmirror() if __name__ == "__main__": unittest.main()