def test_generated_envs(self):
print('Testing generated matrices')
generated_envs = pyopa.generate_all_env(self.log_pam1, 1266)
for i in range(1266):
curr_ref = self.alignment_environments[i]
curr_gen = generated_envs[i]
self.assertAlmostEqual(curr_ref.pam, curr_gen.pam)
self.assertAlmostEqual(curr_ref.threshold, curr_gen.threshold)
self.assertAlmostEqual(curr_ref.gap_open, curr_gen.gap_open)
self.assertAlmostEqual(curr_ref.gap_ext, curr_gen.gap_ext)
for j in range(26):
for k in range(26):
self.assertAlmostEqual(curr_ref.float64_matrix[j][k],
curr_gen.float64_matrix[j][k])
for i in range(20):
for j in range(20):
qsum[i] += json_data['scores'][j][i]
for i in range(20):
json_data['scores'][i][i] = -qsum[i]
return json_data
json_matrix = convert_to_json(os.path.dirname(os.path.abspath(__file__)) + '/test/data/jtt.dat')
for i in range(20):
print(json_matrix['scores'][i])
log_pam1 = pyopa.read_env_json(
os.path.dirname(os.path.abspath(__file__)) + '/test/data/matrices/json/logPAM1.json')
envs = pyopa.read_all_env_json(
os.path.dirname(os.path.abspath(__file__)) + '/test/data/matrices/json/all_matrices.json')
generated_envs = pyopa.generate_all_env(log_pam1, 1266)
mul1 = pyopa.MutipleAlEnv(envs, log_pam1)
mul2 = pyopa.MutipleAlEnv(generated_envs, log_pam1)
s1 = 'PDVRTQYSRTKTIKLAQVRKCGAWRVLCLDLIPDLTAKNNHMRTKWTEVQYLAFVVSIVKKRPLSHSLVLITTGKAWNGTWRALPRLSNKLIETAFKEIQAEETVYDTKAFVAGKKPRWVSPFICYGLPFVISRFDFAQYRLKDMLILFSDMLLSRICNFYNGNTGPVPNSKTNEDTDLFFDGLSGMLKLNLKRSDAICHVICYEAPIARVKFGREVKDKFSLPKGGKNPSRRISWNILGILIDRTMFIRPRLVARKEAIHLFDLIGENIDAITQRLRAHKTLMVHESQVVEQPLKVKNLDLRPELVGEEEKNRHGRAKQLDRMANGNMAQIKNGHFKQTYLISVFRPQWLQLQGGCLIAEGFHSEVGGTVDGLKGTPCAQGPVVKGLFAVWRRCDTLAGRYYQKAADIDKLGDILLASLYYIPQGAIITLSEEMAKRIGANVLLVGLINVRYSGIGYEACVGDLAPEVSWLNAGHGNIQMVLHTIDGDGCQTPHGLKIYTDKRLLDLYQGAQLKVTVATTGSVKVSKSMGWLQEGGLDYFALAGRFYRADLREIEHPRAMAVSAHLCAVGLNWVFLADIICDPNEAFKFGKDFEPRTLTYGFANEDENPKNGGATTTSFAVAVYKIKTVATLKVIGKALWKGIQMRTQQGSGPTCQWALRKGKNSILLLAQDSRGGIPKNEFTILGDLPEGQTTTCTHTEIKTRLLYGATVFFMRGDLVGLYADGCSHLYRSSNLMSQACAAAKTILCSLDGERANFSNPTDFAMYNAVFRPRLYTVSFGVFDNNVDVLQAALYYLIMMAMKQYWGVKQGGLEGTLYTWSKVSGKKETSDSRNNPSICVSVCKNPLKDVQLRIAALKRFAEAEEIGKPAVVIRALEPGLTLYILLSSHGSEGKKTHNPILVSAFVVTTVADTSKPKVTYHKDQEMAIYQVLGNNPAGYEVELAFLLPTASSKQQSGRTRKFMDTASGELKEMPIQSSHEITQAADINNLRQLPRTYKKESAKVKVAACKQPPAALNTGIEKVPSHPDGLQLIIEDEWKLLEASSMSQYNEQAKEWPFHKGGIFFKGHEQKCIDASELPRGITRDLRVILINEALVLNTFCGERKLQNEATLILLRAYVWGRHLLANYFRAPNEQDGVLVDIPQGRSTLKSDHLRASIPLFLYTTIETCTSNVTIHKRVQPMIILDIAVAGEGVCDMKNGQVFKRRMARSNDRRLPPGARMKIILFRRNHECYPLQKHQEQWILGAIRTPYGLYNLQEKATLTTRYLIKLQINNRNDLVTTLVSLLMHTRESYIRFTKERRTTESPIDVLAATLYQEFTREVRRAGEQRAGIFFSQDTNYEQAIFETKMAAYPPFGANSWNPTLRYEAWTIIKTPNSKGQEFFLEHMQDVGYGKIASSKYQEKDDDEEVARGRIVPAWY'
s2 = 'PPFQPDKKLAGIELVLCNADLPGRSIYLRKVLQANANKRASASKRCTDDDIIKVDSAPDPQRKLVQAGKVPRVLYNGDVSNIISQILICAYVTGASRNFQHVMLLMDKGWGRGFTLMVNYPCPKVLEEFNPTLLTALVIISVYLNSIECERAGVTIAALNVKLEATDRLALLGRQTANTVMRAPLLLLCQGDSAKNTLNWSLEDLAIVFGRAATRVCKNLALLLNSQVFFQKTTGYKSQLGKNVINFDLYKPLVCDLVDATKYMKFYGTNDDSTDIQGRSSEKAAALAAAAMGVVGWHFLAPTGLVGAGSTFSPVFCIKGNAQLCCKRFDIDEWKALLTLQKSKIANIDYLRYRTGAVIEVGANYDGCSGQPKLQCFYDYLIRYPETVLGTNRQERVMTDEGGEHVRDLILRNVLENPTGFIGSGTHPGNISCTLETTNADLIIGSTDYDGVGSYLIIMGTCFMVTGCVVFTYAVMELVRPLKIHIFACAKVILQEADGSQKTNLRGRGKVSSFGDLPVRFRTLDGIATPSTTHAEMGASFDAAVLVIGRTGTAKFRQFATLDNRNLACNINLSSIRRYFNDNNWLEAGAKNAAEILVNHADKSLTPWVVGLGPLLKPGDIACPMIAVSYLVLVIMDMYLASYSDSFAKHLKNKHRTTTSAHKPSNQQLALDGALTAKRSSQAASIIFEAEEWGFLEWAMIGHLQTKMIYDDAFRLNSPEEELLTQATTHKIKPNYLIALQMLHRDFCIGFFHTLIHASVADSIVYASRLKQNAAIIDRGKTARQDLLGIALKLIVSASTKNAASFNRDFKLPVDVMFRFLDKMLNHGVNTIVHGGQDPKNGNPVGAGLPSWAKNIKVELQVTMFQLFESVDCTSELRLLSTAVDTTLHGEVQVMSAKDLFGRFRYRILSAGESLMENGISPKSFVEALKYFIMYYWTDITEPRCRGSALYPITIQPNLYKRTSATSLHPKGERWLPFEETSRTTISTVLMNNALLGICLYKSYQLLDHDFLGDKKQSNKRVSENSFLGIQTLHDPTGYLQKLDHSRLSKFNRDIRWGQGKSPEQWAVTLVPTLFVKKGTNAWRKKNNAEPIIVTTGTNTAPLEELHKAWMQLAHDGIVVSTLTENEKLEFFSFQDGMPSLVLFSIMAETNQLRYIGNKIYASRKWMADAQKASWVYASLPTNSCNWTAVEVAFEPKGECQMAKKFDLHSMAIVMVRLLAQERSDGADGMNNASSVKWLRKEANEKVCKWWFASPKINAMFQTVKIQSSGKYLARNPKAATKDVKKVEQDLLSRIQTQEHGLLWFYVRLIGEISEVPILSCNKALFLTIKLFNKFIRWNIAPLEITSGVDAWHTIFTSSRFSETDTGIEMTALDLTLPQGNWGTMKKKVALAATGFILFLAYSMGTLSKKFEGNHHWTW'
print(mul1.estimate_pam(pyopa.Sequence(s1), pyopa.Sequence(s2)))
print(mul2.estimate_pam(pyopa.Sequence(s1), pyopa.Sequence(s2)))
log_pam1_env = defaults['log_pam1']
#the default directory (created at installation time)
matrix_dir = pyopa.matrix_dir()
#or alternatively, you can specify an exact location
env_list = pyopa.read_all_env_json(
os.path.join(matrix_dir, 'all_matrices.json'))
log_pam1_env = pyopa.read_env_json(os.path.join(matrix_dir, 'logPAM1.json'))
#---------------------------------------------------------------------------------------------------
#generates a signle AlignmentEnvironment
# with a pam distance of 250
generated_env = pyopa.generate_env(log_pam1_env, 250)
#generates 1000 environments for different pam distances
gen_env_list = pyopa.generate_all_env(log_pam1_env, 1000)
#---------------------------------------------------------------------------------------------------
s1 = pyopa.Sequence('AATCGGA')
s2 = pyopa.Sequence('AAAA')
s3 = pyopa.Sequence('CATACCTGGTGTGATGCC')
#not optimal, multiple hidden profile generations in the background
print(pyopa.align_short(s1, s2, generated_env))
print(pyopa.align_short(s1, s3, generated_env))
print(pyopa.align_byte(s1, s2, generated_env))
print(pyopa.align_byte(s1, s3, generated_env))
#one profile generation
profile = pyopa.AlignmentProfile()
profile.create_profiles(s1, generated_env)
def setUp(self):
self.log_pam1 = pyopa.read_env_json(os.path.join(pyopa.matrix_dir(), 'logPAM1.json'))
self.env_generated = pyopa.generate_all_env(self.log_pam1, 1266)
self.env_loaded = pyopa.load_default_environments()['environments']