Python SeqUtil.rename Examples

Example #1

File: bac.py Project: solarknow/pevolution

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')

Example #2

File: euk.py Project: solarknow/pevolution

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

Example #3

File: arch.py Project: solarknow/pevolution

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

Example #4

File: all.py Project: solarknow/pevolution

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]
try:
  paml=sys.argv[3]
  paml= paml=='-y'
except IndexError:
  paml=False
print "Beginning alignment"
SeqUtil.rename('Data/all-'+out+'.fas')
os.system('prank -d=Data/all-'+out+' -o=aligns/all-'+out+' -f=nexus -quiet')
SeqUtil.bayesinNex('aligns/all-'+out+'.best.nex')
#SeqUtil.splicealign('aligns/all-'+out+'.best.nex','Bayes/all-'+out+'-mod.nxs')
print "Alignment complete.\nCalculating best model for tree finding"
models_ori=SeqUtil.bestmod('aligns/all-'+out+'.best.nex')
#models=SeqUtil.bestmod('Bayes/all-'+out+'-mod.nxs')
#print models_ori, models
if paml:
  for mod in models.keys():
     SeqUtil.pamlseqnex('Bayes/all-'+out+'-mod.nxs','ML/all-'+out+mod.split('+')[0])
     if models[mod][0]=='0' and models[mod][1]=='0':
         os.system('phyml -i ML/all-'+out+mod.split('+')[0]+' -d aa -b 100 -m '+mod.split('+')[0]+
                   ' -f e -s BEST -u aligns/all-'+out+'.ed.2.dnd -o tl')
     elif models[mod][0]=='0':
         os.system('phyml -i '+'ML/all-'+out+mod.split('+')[0]+' -d aa -b 100 -m '+mod.split('+')[0]+