#!/usr/bin/env python # Copyright (c) 2006 John Gilman # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. from corebio.ssearch_io import * from corebio.ssearch_io import fasta, blastxml from corebio.utils import * from test_corebio import testdata_stream import unittest from StringIO import StringIO class test_search_io(unittest.TestCase) : # def test_report(self) : # rep = Report() def test_Annotation(self) : meta = Annotation() def test_Hit(self) : h = Hit() def test_Alignment(self) : a = Alignment() s = str(a) class test_read(unittest.TestCase) : def test_scan(self) : files = [ testdata_stream("ssearch/xbt001.xml"), testdata_stream("ssearch/xbt002.xml"), testdata_stream("ssearch/xbt003.xml"), testdata_stream("ssearch/xbt004.xml"), testdata_stream("ssearch/xbt005.xml"), testdata_stream("ssearch/ssearch_out.txt"), testdata_stream("ssearch/ssearch_out_compact.txt"), testdata_stream("ssearch/fasta_out_compact.txt"), testdata_stream("ssearch/ssearch_out_compact2_dbvdb.txt"), testdata_stream("ssearch/ssearch_out_compact_dbvdb.txt"), ] results = [read(f) for f in files] self.assertEquals( len(files), len(results) ) class test_blastxml_read(unittest.TestCase) : def examples(self) : files = [ testdata_stream("ssearch/xbt001.xml"), testdata_stream("ssearch/xbt002.xml"), testdata_stream("ssearch/xbt003.xml"), testdata_stream("ssearch/xbt004.xml"), testdata_stream("ssearch/xbt005.xml"), testdata_stream("ssearch/megablast.xml"), ] return files def test_read_empty(self) : f = StringIO() self.assertRaises(ValueError, blastxml.read, f) def test_scan(self) : files = self.examples() reports = [blastxml.read(f) for f in files] self.assertEquals( len(files), len(reports) ) # First report r = reports[0] self.assertEquals( r.algorithm, "blastp" ) self.assertEquals( r.algorithm_version, "2.2.12" ) self.assertEquals( len(r.results[0].hits), 212 ) hit = r.results[0].hits[6] self.assertEquals( hit.target.name, "gi|49609685|emb|CAG73118.1|" ) self.assertEquals( hit.target.length, 86 ) self.assertAlmostEquals( hit.alignments[0].raw_score, 219 ) self.assertAlmostEquals( hit.alignments[0].bit_score, 88.9669 ) self.assertAlmostEquals( hit.alignments[0].significance, 4.10205e-17 ) self.assertEquals("MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEP--KQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV", hit.alignments[0].query_seq) self.assertEquals( "MGGISIWQLLI+AVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDD+ KQDKTSQDADFTAK+IADKQ +AK EDAK DKEQV", r.results[0].hits[5].alignments[0].mid_seq) # Test megablast parseing with two queroes. r = reports[5] self.assertEquals( r.algorithm, "blastn" ) self.assertEquals( r.algorithm_version, "2.2.14" ) self.assertEquals( len(r.results), 2) class test_fasta_read(unittest.TestCase) : def examples(self) : files = [ testdata_stream("ssearch/ssearch_out.txt"), testdata_stream("ssearch/ssearch_out_compact.txt"), testdata_stream("ssearch/fasta_out_compact.txt"), testdata_stream("ssearch/ssearch_out_compact2_dbvdb.txt"), testdata_stream("ssearch/ssearch_out_compact_dbvdb.txt"), ] return files def test_read_empty(self) : f = StringIO() self.assertRaises(ValueError, fasta.read, f) def test_read(self) : files = self.examples() reports = [fasta.read(f) for f in files] self.assertEquals( len(files), len(reports) ) # First report r = reports[0] #print repr(report) self.assertEquals( r.algorithm, "SSEARCH" ) self.assertEquals( r.algorithm_version, "3.4t24" ) self.assertEquals( len(r.results[0].hits), 16 ) # d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 34 15.7 6.9 hit = r.results[0].hits[10] self.assertEquals( hit.target.name, "d8rxna_" ) self.assertEquals( hit.target.length, 52 ) self.assertAlmostEquals( hit.raw_score, 34 ) self.assertAlmostEquals( hit.bit_score, 15.7 ) self.assertAlmostEquals( hit.significance, 6.9 ) #print repr(hit) self.assertEquals( hit.alignments[0].target_seq, 'EGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNG-RPELAFDFKAMKRA..............') # Compact report r = reports[1] self.assertEquals( r.algorithm, "SSEARCH" ) self.assertEquals( r.algorithm_version, "3.4t24" ) self.assertEquals( len(r.results[0].hits), 16 ) # d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 34 15.7 6.9 hit = r.results[0].hits[10] self.assertEquals( hit.target.name, "d8rxna_" ) self.assertEquals( hit.target.length, 52 ) self.assertAlmostEquals( hit.raw_score, 34 ) self.assertAlmostEquals( hit.bit_score, 15.7 ) self.assertAlmostEquals( hit.significance, 6.9 ) # DBvDB report #result = reports[4][1] r = reports[4] self.assertEquals( r.algorithm, "SSEARCH" ) self.assertEquals( r.algorithm_version, "3.4t24" ) self.assertEquals( len(r.results), 23 ) self.assertEquals( len(r.results[1].hits), 21 ) # d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 58 22.0 0.058 ... hit = r.results[1].hits[1] self.assertEquals( hit.target.name, "d2sn3__" ) self.assertEquals( hit.target.length, 65 ) self.assertAlmostEquals( hit.raw_score, 58 ) self.assertAlmostEquals( hit.bit_score, 22 ) self.assertAlmostEquals( hit.significance, 0.058 ) # def test_this(self) : # files = self.examples() # for f in files : # print f # reports = fasta.read(f) # print repr(reports) if __name__ == '__main__': unittest.main()