import os, sys
import SeqUtil, Report
if not os.path.exists('aligns'):
os.mkdir('aligns')
if not os.path.exists('Bayes'):
os.mkdir('Bayes')
#if not os.path.exists('ML'):
# os.mkdir('ML')
out= sys.argv[1]
query = sys.argv[2]
SeqUtil.rename('Data/bac-'+out+'.fas')
if not os.path.exists('aligns/bac-'+out+'.best.nex'):
os.system('prank -d=Data/bac-'+out+' -o=aligns/bac-'+out+' -f=nexus -quiet')
SeqUtil.bayesinNex('aligns/bac-'+out+'.best.nex')
#SeqUtil.splicealign('aligns/bac-'+out+'.best.nex','Bayes/bac-'+out+'-mod.nxs')
#models=SeqUtil.bestmod('Bayes/bac-'+out+'-mod.nxs')
models_ori=SeqUtil.bestmod('aligns/bac-'+out+'.best.nex')
if not os.path.exists('Bayes/bac-'+out+'-bayes.nxs'):
SeqUtil.bayesfile('aligns/bac-'+out+'.best.nex',models_ori,'Bayes/bac-'+out+'-bayes.nxs')
#SeqUtil.bayesfile('Bayes/bac-'+out+'-mod.nxs',models,'Bayes/bac-'+out+'-bayes.nxs')
os.system('mb Bayes/bac-'+out+'-bayes.nxs')
#SeqUtil.pamlseqnex('Bayes/bac-'+out+'-mod.nxs','ML/bac-'+out)
#for mod in models.keys():
# SeqUtil.pamlinput('ML/bac-'+out,'ML/bac-'+out+'.out','ML/bac-'+out+'.ctl',{models.keys()[mod].split('+')[0]:models[models.keys()[mod]][1]})
# os.system('codeml ML/bac-'+out+'.ctl')
# SeqUtil.extractMLtree('ML/bac-'+out+'.out')
Report.generateReport(out,query,models_ori,'bac')
