from __future__ import division import os from cogent.util.unit_test import TestCase, main from cogent.db.ensembl.host import HostAccount, get_ensembl_account from cogent.db.ensembl.compara import Compara __author__ = "Gavin Huttley, Hua Ying" __copyright__ = "Copyright 2007-2009, The Cogent Project" __credits__ = ["Gavin Huttley", "hua Ying"] __license__ = "GPL" __version__ = "1.4.1" __maintainer__ = "Gavin Huttley" __email__ = "Gavin.Huttley@anu.edu.au" __status__ = "alpha" Release = 56 if 'ENSEMBL_ACCOUNT' in os.environ: username, password = os.environ['ENSEMBL_ACCOUNT'].split() account = HostAccount('127.0.0.1', username, password) else: account = get_ensembl_account(release=Release) def calc_slope(x1, y1, x2, y2): """computes the slope from two coordinate sets, assigning a delta of 1 when values are identical""" delta_y = y2-y1 delta_x = x2-x1 delta_y = [delta_y, 1][delta_y == 0] delta_x = [delta_x, 1][delta_x == 0] return delta_y/delta_x class ComparaTestBase(TestCase): comp = Compara(['human', 'mouse', 'rat', 'platypus'], Release=Release, account=account) class TestCompara(ComparaTestBase): def test_query_genome(self): """compara should attach valid genome attributes by common name""" brca2 = list(self.comp.Mouse.getGenesMatching(Symbol="brca2"))[0] self.assertEquals(brca2.Symbol.lower(), 'brca2') def test_get_related_genes(self): """should correctly return the related gene regions from each genome""" brca2 = list(self.comp.Human.getGenesMatching(StableId="ENSG00000139618"))[0] Orthologs = self.comp.getRelatedGenes(gene_region=brca2, Relationship="ortholog_one2one") self.assertEquals("ortholog_one2one", Orthologs.Relationships[0]) def test_get_related_genes2(self): """should handle case where gene is absent from one of the genomes""" clec2d = list(self.comp.Mouse.getGenesMatching( StableId='ENSMUSG00000030157'))[0] orthologs = self.comp.getRelatedGenes(gene_region=clec2d, Relationship='ortholog_one2many') self.assertEquals(len(orthologs.Members),3) def test_get_collection(self): brca2 = list(self.comp.Human.getGenesMatching(StableId="ENSG00000139618"))[0] Orthologs = self.comp.getRelatedGenes(gene_region=brca2, Relationship="ortholog_one2one") collection = Orthologs.getSeqCollection() self.assertTrue(len(collection.Seqs[0])> 1000) def test_getting_alignment(self): mid = "ENSMUSG00000041147" brca2 = list(self.comp.Mouse.getGenesMatching(StableId=mid))[0] result = list(self.comp.getSyntenicRegions(region=brca2, align_method='PECAN', align_clade='vertebrates'))[0] aln = result.getAlignment(feature_types='gene') self.assertTrue(len(aln) > 1000) def test_generate_method_clade_data(self): """should correctly determine the align_method align_clade options for a group of species""" # we should correctly infer the method_species_links, which is a # cogent.util.Table instance self.assertTrue(self.comp.method_species_links.Shape > (0,0)) def test_get_syntenic_returns_nothing(self): """should correctly return None for a SyntenicRegion with golden-path assembly gap""" Start = 100000 End = Start + 100000 related = list(self.comp.getSyntenicRegions(Species='mouse', CoordName='1', Start=Start, End=End, align_method='PECAN', align_clade='vertebrates')) self.assertEquals(related, []) def test_get_species_set(self): """should return the correct set of species""" expect = set(['Homo sapiens', 'Ornithorhynchus anatinus', 'Mus musculus', 'Rattus norvegicus']) brca2 = list(self.comp.Human.getGenesMatching(StableId="ENSG00000139618"))[0] Orthologs = self.comp.getRelatedGenes(gene_region=brca2, Relationship="ortholog_one2one") self.assertEquals(Orthologs.getSpeciesSet(), expect) def test_pool_connection(self): """excercising ability to specify pool connection""" dog = Compara(['chimp', 'dog'], Release=Release, account=account, pool_recycle=1000) class TestSyntenicRegions(TestCase): comp = Compara(['human', 'chimp', 'macaque'], account=account, Release=Release) def test_correct_alignments(self): """should return the correct alignments""" # following cases have a mixture of strand between ref seq and others coords_expected = [ [{'CoordName': 4, 'End': 78099, 'Species': 'human', 'Start': 77999, 'Strand':-1}, {'Homo sapiens:chromosome:4:77999-78099:-1': 'ATGTAAATCAAAACCAAAGTCTGCATTTATTTGCGGAAAGAGATGCTACATGTTCAAAGATAAATATGGAACATTTTTTAAAAGCATTCATGACTTAGAA', 'Macaca mulatta:chromosome:1:3891064-3891163:1': 'ATGTCAATCAAAACCAAAGTCTGTATTTATTTGCAGAAAGAGATACTGCATGTTCAAAGATAAATATGGAAC-TTTTTAAAAAGCATTAATGACTTATAC', 'Pan troglodytes:chromosome:4:102056-102156:-1': 'ATGTAAATCAAAACCAAAGTCTGCATTTATTTGCGGAAAGAGATGCTACATGTTCAAAGATAAATATGGAACATTTTTAAAAAGCATTCATGACTTAGAA'}], [{'CoordName': 18, 'End': 213739, 'Species': 'human', 'Start': 213639, 'Strand':-1}, {'Homo sapiens:chromosome:18:213639-213739:-1': 'ATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTGAGTGCAGATTATTCGGTAAACACT----CTTA', 'Macaca mulatta:chromosome:18:13858303-13858397:1': '------GTTTCCCTTTAGGGCTCTAAGATGAGGTCATCATTGTTTTTAATCCTGAAGAAGGGCTACTGA----GTGCAGATTATTCTGTAAATGTGCTTACTTG', 'Pan troglodytes:chromosome:18:16601082-16601182:1': 'ATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGA----GTGCAGATTATTCTGTAAACACTCACTCTTA'}], [{'CoordName': 5, 'End': 204974, 'Species': 'human', 'Start': 204874, 'Strand':1}, {'Homo sapiens:chromosome:5:204874-204974:1': 'AACACTTGGTATTT----CCCCTTTATGGAGTGAGAGAGATCTTTAAAATATAAACCCTTGATAATATAATATTACTACTTCCTATTA---CCTGTTATGCAGTTCT', 'Macaca mulatta:chromosome:6:1297736-1297840:-1': 'AACTCTTGGTGTTTCCTTCCCCTTTATGG---GAGAGAGATCTTTAAAATAAAAAACCTTGATAATATAATATTACTACTTTCTATTATCATCTGTTATGCAGTTCT', 'Pan troglodytes:chromosome:5:335911-336011:1': 'AACACTTGGTAGTT----CCCCTTTATGGAGTGAGAGAGATCTTTAAAATATAAACCCTTGATAATATAATATTACTACTTTCTATTA---CCTGTTATGCAGTTCT'}], [{'CoordName': 18, 'End': 203270, 'Species': 'human', 'Start': 203170, 'Strand':-1}, {'Homo sapiens:chromosome:18:203170-203270:-1': 'GGAATAATGAAAGCAATTGTGAGTTAGCAATTACCTTCAAAGAATTACATTTCTTATACAAAGTAAAGTTCATTACTAACCTTAAGAACTTTGGCATTCA', 'Macaca mulatta:chromosome:18:13869026-13869126:1': 'GGAATAATGAAAGCAATTGTAAGTTAGCAATTACCTTCAAAGAATTACATTTCTTATACAAAGTAAAGTTCATTACTAACCTTAAGAACTTTGGCATTCA', 'Pan troglodytes:chromosome:18:16611584-16611684:1': 'GGAATAATGAAAGCAATTGTAAGTTAGCAATTACCTTCAAAGAATTACATTTCTTATACAAAGTAAAGTTCATTACTAACCTTAAGAACTTTGGCATTCA'}], [{'CoordName': 2, 'End': 46445, 'Species': 'human', 'Start': 46345, 'Strand':-1}, {'Homo sapiens:chromosome:2:46345-46445:-1': 'CTACCACTCGAGCGCGTCTCCGCTGGACCCGGAACCCCGGTCGGTCCATTCCCCGCGAAGATGCGCGCCCTGGCGGCCCTGAGCGCGCCCCCGAACGAGC', 'Macaca mulatta:chromosome:13:43921-44021:-1': 'CTGCCACTCCAGCGCGTCTCCGCTGCACCCGGAGCGCCGGCCGGTCCATTCCCCGCGAGGATGCGCGCCCTGGCGGCCCTGAACACGTCGGCGAGAGAGC', 'Pan troglodytes:chromosome:2a:36792-36892:-1': 'CTACCACTCGAGCGCGTCTCCGCTGGACCCGGAACCCCAGTCGGTCCATTCCCCGCGAAGATGCGCGCCCTGGCGGCCCTGAACGCGCCCCCGAACGAGC'}], [{'CoordName': 18, 'End': 268049, 'Species': 'human', 'Start': 267949, 'Strand':-1}, {'Homo sapiens:chromosome:18:267949-268049:-1': 'GCGCAGTGGCGGGCACGCGCAGCCGAGAAGATGTCTCCGACGCCGCCGCTCTTCAGTTTGCCCGAAGCGCGGACGCGGTTTACGGTGAGCTGTAGAGGGG', 'Macaca mulatta:chromosome:18:13805604-13805703:1': 'GCGCAG-GGCGGGCACGCGCAGCCGAGAAGATGTCTCCGACGCCGCCGCTCTTCAGTTTGCCCGAAGCGCGGACGCGGTTTACGGTGAGCTGTAGGCGGG', 'Pan troglodytes:chromosome:18:16546800-16546900:1': 'GCGCAGTGGCGGGCACGCGCAGCCGAGAAGATGTCTCCGACGCCGCCGCTCTTCAGTTTGCCCGAAGCGCGGACGCGGTTTACGGTGAGCTGTAGCGGGG'}], [{'CoordName': 16, 'End': 107443, 'Species': 'human', 'Start': 107343, 'Strand':-1}, {'Homo sapiens:chromosome:16:107343-107443:-1': 'AAGAAGCAAACAGGTTTATTTTATACAGTGGGCCAGGCCGTGGGTCTGCCATGTGACTAGGGCATTTGGACCTAGGGAGAGGTCAGTCTCAGGCCAAGTA', 'Pan troglodytes:chromosome:16:48943-49032:-1': 'AAGAAGCAAACAGGTTTATTTTATACACTGGGCCAGGCCGTGGGTCTGCCATGTGACTAGGGAATTTGGACC-----------CAGTCTCAGGCCAAGTA'}] ] for coord, expect in coords_expected[1:]: hum_length = coord['End'] - coord['Start'] syntenic = list( self.comp.getSyntenicRegions(method_clade_id=435, **coord))[0] # check the slope computed from the expected and returned # coordinates is ~ 1 got_names = dict([(n.split(':')[0], n.split(':')) for n in syntenic.getAlignment().Names]) exp_names = dict([(n.split(':')[0], n.split(':')) for n in expect.keys()]) for species in exp_names: exp_chrom = exp_names[species][2] got_chrom = got_names[species][2] self.assertEquals(exp_chrom, got_chrom) exp_start, exp_end = map(int, exp_names[species][3].split('-')) got_start, got_end = map(int, got_names[species][3].split('-')) slope = calc_slope(exp_start, exp_end, got_start, got_end) self.assertFloatEqual(abs(slope), 1.0) def test_failing_region(self): """should correctly handle queries where multiple Ensembl have genome block associations for multiple coord systems""" gene = list(self.comp.Human.getGenesMatching( StableId='ENSG00000188554'))[0] # this should simply not raise any exceptions syntenic_regions = list(self.comp.getSyntenicRegions(region=gene, align_method='PECAN', align_clade='vertebrates')) if __name__ == "__main__": main()