#!/usr/bin/env python """Tests for FastTree v1.0.0 application controller""" from shutil import rmtree from os import getcwd from cogent.util.unit_test import TestCase, main from cogent.app.fasttree_v1 import FastTree, build_tree_from_alignment from cogent.core.alignment import Alignment from cogent.parse.fasta import MinimalFastaParser from cogent.parse.tree import DndParser from cogent.core.moltype import DNA __author__ = "Daniel McDonald" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["Daniel McDonald"] __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "Daniel McDonald" __email__ = "mcdonadt@colorado.edu" __status__ = "Development" class FastTreeTests(TestCase): def setUp(self): self.seqs = Alignment(dict(MinimalFastaParser(test_seqs.split()))) def test_base_command(self): app = FastTree() self.assertEqual(app.BaseCommand, \ ''.join(['cd "',getcwd(),'/"; ','FastTree'])) app.Parameters['-nt'].on() self.assertEqual(app.BaseCommand, \ ''.join(['cd "',getcwd(),'/"; ','FastTree -nt'])) def test_change_working_dir(self): app = FastTree(WorkingDir='/tmp/FastTreeTest') self.assertEqual(app.BaseCommand, \ ''.join(['cd "','/tmp/FastTreeTest','/"; ','FastTree'])) rmtree('/tmp/FastTreeTest') def test_build_tree_from_alignment(self): tree = build_tree_from_alignment(self.seqs, DNA) for o,e in zip(tree.traverse(), DndParser(exp_tree).traverse()): self.assertEqual(o.Name,e.Name) self.assertFloatEqual(o.Length,e.Length) test_seqs = """>test_set1_0 GGTAGATGGGACTACCTCATGACATGAAACTGCAGTCTGTTCTTTTATAGAAGCTTCATACTTGGAGATGTATACTATTA CTTAGGACTATGGAGGTATA >test_set1_1 GGTTGATGGGACTACGTAGTGACATGAAATTGCAGTCTGTGCTTTTATAGAAGTTTGATACTTGGAGCTCTCTACTATTA CTTAGGACTATGGAGGTATA >test_set1_2 GGTTGATGGGCCTACCTCATGACAATAAACTGAAGTCTGTGCTTTTATAGAGGCTTGATACTTGGAGCTCTATACTATTA CTTAGGATTATGGAGGTCTA >test_set1_3 GGTTGATGGGACTACCTCATGACATGAAACTGCAGTCTGTGCTTTTATAGAAGCTTGATACTTGGAGATCTATACTATTA CTTAGGACTATGGAGGTCAC >test_set1_4 GGTTGGTGGGACTACCTCATGACATGAAGATGCAGTCTGTGCTTGTATAGAAGCTTGAAACTTGGATATCTATACTATTA CTTAAGACTATGGAGGTCTA >test_set1_5 GGTTGATGCGACTACCTCATGACATGAGACTGCAGTCTGTGCTTTTACTGAAGCTTGATACTTGGAGATCTATACTATTA CTTAGGACTATGGAGGTTTA >test_set1_6 GGTTGATGGGACTACCTCATGACATGAAAATGCAGTCTGTCCTTTTATAGAAGCTTGATACTTGTAGATCTATACTGTTA CTTAGGACTATGGAGGTCTA >test_set1_7 GGTTGATGGGACTCCCTCATGACATAAAACTGCAGTCTGTGCTTTTACAGAAGCTTGATACTTGGAGATCTATACTATTA CATAGGACTATGGAGGTCTA >test_set1_8 GGTTGATGGCACTACCTCATGAGATGAAACTGCAGTCTGTGCTTTTATAGAAGCTTGATACTTGGATATCTATACTATAA CTTAGTACTATGGAGGCCTA >test_set1_9 GGTTTATGTTACTACCTCATGACATGAAACGGCAGCATGTGCTTTTATAGAAGCTTGATACTTGGAGATCTAAACTATTA CTTAGGACTATGGAGGTCTA >test_set2_0 AGCGAATCATACTCTGGAAAGAAAAGGACGACTCCTTTGCTCGCGGTCTAGCTGCTACAGCTTCACCGAGTACATCTGAA TGATGGTTGAACCGGGTTCA >test_set2_1 AGAGAATAGTACTCTGGAAAGACAAGGACGACTCCTTTGATCGCGGTCTAGCTGCTACAGCTTCACCGAGTACATCTGAA TGATGGTTGAACCGGATTCA >test_set2_2 AGAGTATAATACTCTGGAAAGAAAAGGACGACTCCTTTGATCGCGGTCTAGCTGCTACAGCTTCACCGAGTACATCTTAA TGATGGTTGAACCGGGGTCA >test_set2_3 AGAGAATCATACTCTGGAAAGAAATGGACGACTCCTTTGATCGCGGTCCAGCTGCTACAGCTTCACCGAGTACATCTGAA TGATGGTTGGACCGGGTTCA >test_set2_4 AGAGAATAATAGTCTGGAAAGAAAAGGACGACTCCTTTGTTCCCGGTCTAGCTGCTACAGCTTCCCCGAGTACATCTGAA TGATGGTTGAACCGGGTTCA >test_set2_5 ACAGAATACTACTCTGGAAAGAAAAGGCCGACTCCTTTGATCGCTGTCTAGCTGCGACAGCTGCACGGAGTCCATCCGAA TGATGGTTGAACCGGGTTCA >test_set2_6 AGAGAATAATACTCTGGACAGAAATGGACGACTCCTTTGATCGCGGTCTAGCTGCTACAGCTTCACCGAGTACATCTGAA TGATGGCTGAACCGGGTTCA >test_set2_7 AGAGAATATTACTCTGGAAAGAAAAGGACGACTCCTTGGATCGCGGTCTAGCTGCTACAGCTTCAGCGAGTACATCGGAA TGATGGTTTAACCGGGTTCA >test_set2_8 AGTGAATAATACTCTGGAAAGAAAAGGACGACTCCTTTGATCGCGGTCTAGCTGCTAGAGCTTCACCGAGTACATCTGAA TGATGGTTGAACCGGGTTCA >test_set2_9 AGAGATTAATACTCTGGATAGAAAATGACGACTCCTTTGATCGCGGTCTAGCTGCTACAGATTGACCTATTACATCTGAA TGATGGTTGAACCGGGTTCA >test_set3_0 TTGTCTCCATTGAGCACTCTAATCTTGCCGTGTATTCAGGAAAGGAGGATAGAACTCGGACAGTATTCTGAACATTACAG AATCGCCGTATTTACGGTGT >test_set3_1 TTGTCTCCATTGAGCACTCTAATCATGCCGTGTATTCAGGAACGGAGGAGAGGACTCGGTCAGTATTCGGAACATTACAG AATGGCGTTATTTACGGTGT >test_set3_2 TTGTCTCCATTGAGCACTCTAATCTTGCCGTGTATTCAGGAACGGAGGATAGAACTCGGACAGAATCCTGAATATTACAA AATCGGGTTATTTACGGTGT >test_set3_3 TTGTCTCCATTGAGCACTCTAATCTTGCCGTGTTTTCAGGAACGGAGGATAGAACTCGGACAGTAGCCTGAACATTACAG AATCCCGTTATTTACGGTGT >test_set3_4 TTGTCTCCATCGAGCACTCTAATCTTGCCGTGTATTCAGGAACGGAGGATTGAACTCGGACAGTATCCTGAACATTACAG AATCGCGTTATTTACGGTGT >test_set3_5 TTGTCTCCATTGAGCACGCTAAGCTTGCCGTGTATTCAGGAACGGAGGATAGAACTCGGACAGTATCCTGAACATTACAG AATCGCGTTATTTACGGTGT >test_set3_6 TTGTCGTCATTGAGCACTCTAATCTTGCCGTGTATTCAGGAACGAAGGATAGAACTCGGACAGTATCCTGAACTTTGCAA AATCGCGTTATTTACGGTGT >test_set3_7 TTGTCTCCATTGAGCACTCTAATCTAGCCGTGTAGTCAGGAACGGAGGATGGAACGCGCACAGTATCCTGAACATAACAG AATCGCGTTATTTACGGTGT >test_set3_8 TTGTCTCCATTGAGCACTCTAATCTTGCCGTATATTCCCGAACGGAGGATAGAACTCGGACAGTAGCCTGAACAGTACAG AATCGCGTTATTTACGGTGT >test_set3_9 TTGTCTCCCTTGAGCACTCTAATCTTGCCGTGTATTCAGGAACGGAGGATAGAACTCGGACAGTATCCTGAACATTACAG AATCGCGTTATTTACGGTGT >test_set4_0 CTTTTACCGGGCTGCCCGAGAGCACTATCTGCGTCGTGCCCTGCTTCGATGCCCACACTACCATCATACTATTCGTGAAT TTGCGGCCGCTAAGATCCGA >test_set4_1 CTTTTATCGGGGTGCCTGATAGCACCATCTGCGTCGTGCCCTGCTTCGATGCCTAAACCACCGTCATGCTATTTGTGAAT TTGAGGTCGCTAAGAGCCCA >test_set4_2 CTTTTATCGGGGTGCCCGAGAGCACCATCTGCGTCGTGCCCTGCTTCGATGCCCAGGCCACCATCATACTATTTGTGGCT TAGGGGTCGCTAAGAGCCGA >test_set4_3 CTTTTATCGGGGGGCCCGAGAGCACCACCTGCGTCGTGCCCTGCTTCGATGCCCAAACCACCATCATACTATTTGTGAAT TTGGGGTCGCTAAGAGCCGA >test_set4_4 CTTTTATAGGGGTGCCCGAGAGCACCATCTGCGTCGTGCCCAGCTTCGATTTCCAAACCACCATCATACTATTTGTGAAC TTGGGGACGTTAAGAGCCGA >test_set4_5 CTTTTCGCGGGGTGCCCGAGAGCACCATCTGCGTCGCGCCCTGCTTCGGTGCCCATACCACCATCATAATATTTGGGAAA TTGGGATCGCTAAGAGTCGA >test_set4_6 CTTTTCTCGGGGTGCCCGAGAGCCCCATCTGCGTTGTGCCCTGCTACTATGCCCAAACCACCATCATACTATTTGTGAAT GTGGCGTCGCTCAGAGCCGA >test_set4_7 CTTTTATCGGGGTGCCCGAGAGCACCATCTGCGTCGTGCCCTGCTTCGATGCCCACGTCACCATACTACTATTTGTGAAT TTGGGGTCGCTAATAGCCGA >test_set4_8 CTTTTATCGGGGGGCCCGAGAGCATCATCTGCGTCGTGCCCTGCTTCGATGCCCAAACTACCATCATACTATTTGTGAAT TTGGGGTTTCTAAGAGCCGA >test_set4_9 CTTTTACCGGGGTGACCGAGAGCACCATCTGCGCCGTGCCCTGCTTCGAGGCCCAAACCACCATCATACTGTTTGTGAAT CAGGGGTTGCTAAGAGCCGA""" exp_tree = """(test_set1_3:0.02062,(test_set1_8:0.05983,test_set1_9:0.07093)0.652:0.00422,((test_set1_5:0.04140,test_set1_7:0.03208)0.634:0.00995,((test_set1_0:0.04748,(test_set1_1:0.07025,(test_set1_2:-0.00367,((((((test_set3_4:0.01485,test_set3_7:0.05863)0.862:0.00569,(test_set3_5:0.02048,(test_set3_3:0.02036,test_set3_8:0.04218)0.724:0.01088)0.397:0.00005)0.519:0.00018,((test_set3_0:0.03139,test_set3_1:0.06448)0.699:0.01095,test_set3_9:0.00940)0.505:0.00036)0.721:0.01080,test_set3_6:0.05333)0.808:0.16470,test_set3_2:-0.12547)1.000:1.42295,((test_set4_1:-0.24707,((test_set4_3:0.00903,test_set4_8:0.04272)0.650:0.00955,(test_set4_4:0.07633,((test_set4_5:0.09853,test_set4_6:0.08143)0.577:0.00748,((test_set4_0:0.08822,test_set4_9:0.07914)0.371:0.00130,(test_set4_2:0.03477,test_set4_7:0.04983)0.764:0.01228)0.665:0.00370)0.535:0.00147)0.633:0.00116)0.850:0.32065)0.998:1.45908,(((test_set2_2:0.03125,((test_set2_8:0.01770,(test_set2_0:0.02172,test_set2_4:0.04082)0.482:0.00228)0.575:0.00249,(test_set2_9:0.07291,(test_set2_3:0.03201,test_set2_6:0.01973)0.538:0.00746)0.690:0.00319)0.746:0.00073)0.788:0.00569,(test_set2_5:0.08827,test_set2_7:0.04250)0.717:0.00533)0.504:0.04532,test_set2_1:-0.01642)0.997:1.14023)0.625:0.41298)0.822:0.20836)0.783:0.07781)0.487:0.00591)0.469:0.00151,(test_set1_4:0.06606,test_set1_6:0.02981)0.703:0.00956)0.560:0.00216)0.468:0.00050);""" if __name__ == '__main__': main()