convert_matrix.py

import json
import pyopa
import os


def convert_to_json(matrix_file):
    with open(matrix_file) as f:
        json_data = {
            'column_order': [
                "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"],
            'scores': [[0 for i in range(20)] for i in range(20)]
        }

        tmp_score_matrix = []

        for i in range(19):
            tmp_score_matrix.append([0] * (i + 1))
            tmp_scores = [float(x) for x in f.readline().split()]

            for j in range(i + 1):
                tmp_score_matrix[i][j] = tmp_scores[j]

        line = f.readline()
        while not line.strip():
            line = f.readline()

        tmp_frequencies = [float(x) for x in line.split()]
        sum_freq = sum(tmp_frequencies)
        #sum should be 1
        json_data['frequencies'] = [x/sum_freq for x in tmp_frequencies]

        for i in range(20):
            for j in range(i):
                json_data['scores'][i][j] = tmp_score_matrix[i-1][j] * json_data['frequencies'][i]
                json_data['scores'][j][i] = tmp_score_matrix[i-1][j] * json_data['frequencies'][j]

        qsum = [0] * 20
        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)))