def copy_files_for_replica(ds_path, out_ds_path, rep, names, alg, ds_name):
reference_seq_name = (
os.path.join(ds_path, "R%d" % rep, names[CODE_SEQ]) if not use_initial
and not is_alignment_available(alg) else os.path.join(
twophase_conf.get("initial", "alignment"), ds_name, "R%d" %
rep, "%s_%s" % (use_initial_alg_ml, use_initial_alg), ALIGNED))
out_seq_path = os.path.join(out_ds_path, INPUT)
if IGNORE_MISSING_OPTIONAL_FILES or os.path.exists(reference_seq_name):
os.system('ln -sf %s %s' % (reference_seq_name, out_seq_path))
else:
raise RuntimeError("path %s does not exists." % reference_seq_name)
if is_data_available(CODE_REFTREE):
reference_tree_name = os.path.join(ds_path, "R%d" % rep,
names[CODE_REFTREE])
out_tree_path = os.path.join(out_ds_path, "reference.tre")
if os.path.exists(reference_tree_name):
os.system('ln -sf %s %s' % (reference_tree_name, out_tree_path))
else:
raise RuntimeError("path %s does not exists." %
reference_tree_name)
if is_data_available(CODE_REFALG):
reference_alg_name = os.path.join(ds_path, "R%d" % rep,
names[CODE_REFALG])
out_alg_path = os.path.join(out_ds_path, "reference.fasta")
if os.path.exists(reference_alg_name):
os.system('ln -sf %s %s' % (reference_alg_name, out_alg_path))
else:
raise RuntimeError("path %s does not exists." % reference_alg_name)
if is_alignment_available(alg):
m = twophase_conf.get("initial", "alignment")
'''copy the spfn file over'''
if is_data_available(CODE_REFALG):
copyfile(
os.path.join(twophase_conf.get("initial", "alignment"),
ds_name, "R%d" % rep,
"%s_%s" % (use_initial_alg_ml, use_initial_alg),
SPFN_STAT), os.path.join(out_ds_path, SPFN_STAT))
'''copy the alignment stat over'''
src_path = os.path.join(
twophase_conf.get("initial", "alignment"), ds_name, "R%d" % rep,
"%s_%s" % (use_initial_alg_ml, use_initial_alg), ALG_STAT)
if os.path.exists(src_path) or not IGNORE_MISSING_OPTIONAL_FILES:
copyfile(src_path, os.path.join(out_ds_path, ALG_STAT))
if use_initial:
'''alignment time needs to be added with initial alignment time'''
inital_stat_file = os.path.join(
twophase_conf.get("initial", "alignment"), ds_name, "R%d" % rep,
"%s_%s" % (use_initial_alg_ml, use_initial_alg), ALG_STAT)
if os.path.exists(inital_stat_file):
copyfile(inital_stat_file,
os.path.join(out_ds_path, "initial_%s" % ALG_STAT))
else:
print >> sys.stderr, "Could not find initial alignment statistics file: %s" % inital_stat_file
def copy_files_for_replica(ds_path, out_ds_path, rep, names, alg, ds_name):
reference_seq_name = (os.path.join(ds_path, "R%d" % rep, names[CODE_SEQ])
if not use_initial and not is_alignment_available(alg) else
os.path.join(twophase_conf.get("initial", "alignment"),
ds_name, "R%d" % rep,
"%s_%s" %(use_initial_alg_ml,use_initial_alg), ALIGNED))
out_seq_path = os.path.join(out_ds_path, INPUT)
if IGNORE_MISSING_OPTIONAL_FILES or os.path.exists(reference_seq_name):
os.system('ln -sf %s %s' % (reference_seq_name, out_seq_path))
else:
raise RuntimeError("path %s does not exists." %reference_seq_name)
if is_data_available(CODE_REFTREE):
reference_tree_name = os.path.join(ds_path, "R%d" % rep, names[CODE_REFTREE])
out_tree_path = os.path.join(out_ds_path, "reference.tre")
if os.path.exists(reference_tree_name):
os.system('ln -sf %s %s' % (reference_tree_name, out_tree_path))
else:
raise RuntimeError("path %s does not exists." %reference_tree_name)
if is_data_available(CODE_REFALG):
reference_alg_name = os.path.join(ds_path, "R%d" % rep, names[CODE_REFALG])
out_alg_path = os.path.join(out_ds_path, "reference.fasta")
if os.path.exists(reference_alg_name):
os.system('ln -sf %s %s' % (reference_alg_name, out_alg_path))
else:
raise RuntimeError("path %s does not exists." %reference_alg_name)
if is_alignment_available(alg):
m = twophase_conf.get("initial", "alignment")
'''copy the spfn file over'''
if is_data_available(CODE_REFALG):
copyfile(os.path.join(twophase_conf.get("initial", "alignment"),
ds_name, "R%d" % rep,
"%s_%s" %(use_initial_alg_ml,use_initial_alg), SPFN_STAT),
os.path.join(out_ds_path, SPFN_STAT))
'''copy the alignment stat over'''
src_path = os.path.join(twophase_conf.get("initial", "alignment"),
ds_name, "R%d" % rep,
"%s_%s" %(use_initial_alg_ml,use_initial_alg), ALG_STAT)
if os.path.exists(src_path) or not IGNORE_MISSING_OPTIONAL_FILES:
copyfile(src_path,
os.path.join(out_ds_path, ALG_STAT))
if use_initial:
'''alignment time needs to be added with initial alignment time'''
inital_stat_file = os.path.join(twophase_conf.get("initial", "alignment"),
ds_name, "R%d" % rep,
"%s_%s" %(use_initial_alg_ml,use_initial_alg), ALG_STAT)
if os.path.exists(inital_stat_file):
copyfile(inital_stat_file,
os.path.join(out_ds_path, "initial_%s"%ALG_STAT))
else:
print >>sys.stderr, "Could not find initial alignment statistics file: %s" % inital_stat_file
def copy_files_for_replica(ds_path, out_ds_path, rep, names, alg, ds_name):
reference_seq_name = (
os.path.join(ds_path, "R%d" % rep, names[CODE_SEQ]) if not use_initial
and not is_alignment_available(alg) else os.path.join(
twophase_conf.get("initial", "alignment"), ds_name, "R%d" % rep,
"%s_%s" % (DUMMY, use_initial_alg), ALIGNED))
out_seq_path = os.path.join(out_ds_path, INPUT)
if os.path.exists(reference_seq_name):
os.system('ln -sf %s %s' % (reference_seq_name, out_seq_path))
else:
raise RuntimeError("path %s does not exists." % reference_seq_name)
if is_data_available(CODE_REFTREE):
reference_tree_name = os.path.join(ds_path, "R%d" % rep,
names[CODE_REFTREE])
out_tree_path = os.path.join(out_ds_path, "reference.tre")
if os.path.exists(reference_tree_name):
os.system('ln -sf %s %s' % (reference_tree_name, out_tree_path))
else:
raise RuntimeError(
"path %s does not exists." % reference_tree_name)
if is_data_available(CODE_REFALG):
reference_alg_name = os.path.join(ds_path, "R%d" % rep,
names[CODE_REFALG])
out_alg_path = os.path.join(out_ds_path, "reference.fasta")
if os.path.exists(reference_alg_name):
os.system('ln -sf %s %s' % (reference_alg_name, out_alg_path))
else:
raise RuntimeError("path %s does not exists." % reference_alg_name)
if is_alignment_available(alg):
'''copy the spfn file over'''
copyfile(
os.path.join(
twophase_conf.get("initial", "alignment"), ds_name,
"R%d" % rep, "%s_%s" % (DUMMY, use_initial_alg), SPFN_STAT),
os.path.join(out_ds_path, SPFN_STAT))
'''copy the alignment stat over'''
copyfile(
os.path.join(
twophase_conf.get("initial", "alignment"), ds_name,
"R%d" % rep, "%s_%s" % (DUMMY, use_initial_alg), ALG_STAT),
os.path.join(out_ds_path, ALG_STAT))
if use_initial:
'''alignment time needs to be added with initial alignment time'''
copyfile(
os.path.join(
twophase_conf.get("initial", "alignment"), ds_name,
"R%d" % rep, "%s_%s" % (DUMMY, use_initial_alg), ALG_STAT),
os.path.join(out_ds_path, "initial_%s" % ALG_STAT))
def copy_files_for_replica(ds_path, out_ds_path, rep, names, alg, ds_name):
reference_seq_name = (
os.path.join(ds_path, "R%d" % rep, names[CODE_SEQ]) if not use_initial
and not is_alignment_available(alg) else os.path.join(
twophase_conf.get("initial", "alignment"), ds_name, "R%d" %
rep, "%s_%s" % (DUMMY, use_initial_alg), ALIGNED))
out_seq_path = os.path.join(out_ds_path, INPUT)
if os.path.exists(reference_seq_name):
os.system('ln -sf %s %s' % (reference_seq_name, out_seq_path))
else:
raise RuntimeError("path %s does not exists." % reference_seq_name)
if is_data_available(CODE_REFTREE):
reference_tree_name = os.path.join(ds_path, "R%d" % rep,
names[CODE_REFTREE])
out_tree_path = os.path.join(out_ds_path, "reference.tre")
if os.path.exists(reference_tree_name):
os.system('ln -sf %s %s' % (reference_tree_name, out_tree_path))
else:
raise RuntimeError("path %s does not exists." %
reference_tree_name)
if is_data_available(CODE_REFALG):
reference_alg_name = os.path.join(ds_path, "R%d" % rep,
names[CODE_REFALG])
out_alg_path = os.path.join(out_ds_path, "reference.fasta")
if os.path.exists(reference_alg_name):
os.system('ln -sf %s %s' % (reference_alg_name, out_alg_path))
else:
raise RuntimeError("path %s does not exists." % reference_alg_name)
if is_alignment_available(alg):
'''copy the spfn file over'''
copyfile(
os.path.join(twophase_conf.get("initial",
"alignment"), ds_name, "R%d" % rep,
"%s_%s" % (DUMMY, use_initial_alg), SPFN_STAT),
os.path.join(out_ds_path, SPFN_STAT))
'''copy the alignment stat over'''
copyfile(
os.path.join(twophase_conf.get("initial",
"alignment"), ds_name, "R%d" % rep,
"%s_%s" % (DUMMY, use_initial_alg), ALG_STAT),
os.path.join(out_ds_path, ALG_STAT))
if use_initial:
'''alignment time needs to be added with initial alignment time'''
copyfile(
os.path.join(twophase_conf.get("initial",
"alignment"), ds_name, "R%d" % rep,
"%s_%s" % (DUMMY, use_initial_alg), ALG_STAT),
os.path.join(out_ds_path, "initial_%s" % ALG_STAT))
def make_alignment_condor_file(outpath, alg_tool, ds_name, alg):
conf = twophase_conf.get("alignment", alg)
ver = "*"
if conf.startswith("@"):
ver = conf[1:]
conf = ""
alg_tool_path = get_tool_path(alg_tool, ver)
if conf is not None and conf != "":
config_temp = (open(os.path.join(config_path, conf)).read().format(
ftmodel=get_model_string("fasttree", ds_name),
rxmodel=get_model_string("raxml", ds_name, g="CAT")))
out = open(os.path.join(outpath, conf), "w")
out.write(config_temp)
out.close()
condor_temp = (open(
os.path.join(condor_templates_path, "condor.%s" % alg_tool)).read()
if os.path.exists(
os.path.join(condor_templates_path, "condor.%s" %
alg_tool)) else condor_temp_def)
condor_alg = condor_temp.format(
exe=alg_tool_path,
input=INPUT,
output=ALIGNED,
home=HOME,
options=conf,
name="alg")
out = open(os.path.join(outpath, "condor.align"), "w")
out.write(condor_alg)
out.close()
def make_ML_condor_file(outpath, ml_tool,ds_name,ml, outgroup):
conf = twophase_conf.get("ML",ml)
ver = "*"
if conf.startswith("@"):
ver = conf[1:]
conf =""
ml_tool_path = get_tool_path(ml_tool,ver)
condor_temp = (open(os.path.join(condor_templates_path, "condor.%s" % ml_tool)).read()
if os.path.exists(os.path.join(condor_templates_path, "condor.%s" % ml_tool))
else condor_temp_def)
if outgroup is not None and outgroup != "":
outg = "-o %s" %outgroup
else:
outg = ""
condor_ml = condor_temp.format(exe=ml_tool_path,
input="aligned.phylip",
output="ml",
home=HOME,
options=outpath,
name="ml",
model= get_model_string(ml_tool, ds_name),
outgroup=outg)
out = open(os.path.join(outpath, "condor.ml"), "w")
out.write(condor_ml)
out.close()
def make_alignment_condor_file(outpath, alg_tool, ds_name, alg):
conf = twophase_conf.get("alignment", alg)
ver = "*"
if conf.startswith("@"):
ver = conf[1:]
conf = ""
alg_tool_path = get_tool_path(alg_tool, ver)
if conf is not None and conf != "":
config_temp = (open(os.path.join(config_path, conf)).read().format(
ftmodel=get_model_string("fasttree", ds_name),
rxmodel=get_model_string("raxml", ds_name, g="CAT")))
out = open(os.path.join(outpath, conf), "w")
out.write(config_temp)
out.close()
condor_temp = (open(
os.path.join(condor_templates_path, "condor.%s" %
alg_tool)).read() if os.path.exists(
os.path.join(condor_templates_path, "condor.%s" %
alg_tool)) else condor_temp_def)
condor_alg = condor_temp.format(exe=alg_tool_path,
input=INPUT,
output=ALIGNED,
home=HOME,
options=conf,
name="alg")
out = open(os.path.join(outpath, "condor.align"), "w")
out.write(condor_alg)
out.close()
def make_ST_condor(outpath, st_tool,ds_name,st,num):
conf = twophase_conf.get("ST",st)
ver = "*"
if conf.startswith("@"):
ver = conf[1:]
conf =""
tool_path = get_tool_path(st_tool,ver)
condor_temp = open(os.path.join(condor_templates_path, "condor.%s" % st_tool)).read()
main = condor_temp[0:-95]
main = main.format(name="MLBS",
exe=tool_path)
args = condor_temp[-95:-1]
a = []
for bs in range(1,num+1):
a.append( args.format(options="BS/BS.%d"%bs,
input="allele.table",
name="BS.%d" %bs))
condor_temp = main + "\n".join(a)
out = open(os.path.join(outpath, "condor.st"), "w")
out.write(condor_temp)
out.close()
def get_model_string(ml, ds_name, **kwargs):
model = (twophase_conf.get("MODELS", "default.model") if
(not twophase_conf.has_option(
"MODELS", "override.default.model.%s" % ds_name)
or twophase_conf.get(
"MODELS", "override.default.model.%s" % ds_name) == '') else
twophase_conf.get("MODELS",
"override.default.model.%s" % ds_name))
model = (model if not twophase_conf.has_option(
"MODELS", "%s.name.model.%s" % (ml, model)) else twophase_conf.get(
"MODELS", "%s.name.model.%s" % (ml, model)))
dt = twophase_conf.get("MODELS", "default.DT")
dt = (dt
if not twophase_conf.has_option("MODELS", "%s.name.DT.%s" % (ml, dt))
else twophase_conf.get("MODELS", "%s.name.DT.%s" % (ml, dt)))
g = (twophase_conf.get("MODELS", "default.G")
if not kwargs.has_key("g") else kwargs["g"])
g = (g if not twophase_conf.has_option("MODELS", "%s.name.G.%s" % (ml, g))
else twophase_conf.get("MODELS", "%s.name.G.%s" % (ml, g)))
f = twophase_conf.get("MODELS", "default.F")
f = (f if not twophase_conf.has_option("MODELS", "%s.name.F.%s" % (ml, f))
else twophase_conf.get("MODELS", "%s.name.F.%s" % (ml, f)))
i = twophase_conf.get("MODELS", "default.I")
i = (i if not twophase_conf.has_option("MODELS", "%s.name.I.%s" % (ml, i))
else twophase_conf.get("MODELS", "%s.name.I.%s" % (ml, i)))
modelString = (twophase_conf.get("MODELS", "%s.pattern" % ml).format(
DT=dt, G=g, F=f, I=i, model=model) if twophase_conf.has_option(
"MODELS", "%s.pattern" % ml) else "")
#print modelString
return modelString
config_path = os.path.join(CONFPATH, "config_files")
CODE_SEQ = 0
CODE_REFTREE = 1
CODE_REFALG = 2
DUMMY = "dummy"
ALIGNED = "aligned.fasta"
INPUT = "input.fasta"
INITIAL_PREF = "initial."
SPFN_STAT = "spfn.stat"
ALG_STAT = "alg.stat"
condor_templates_path = os.path.join(CONFPATH, "condor_templates")
condor_temp_def = open(os.path.join(condor_templates_path,
"condor.default")).read()
use_initial = twophase_conf.getboolean("initial", "use_initial")
use_initial_alg = twophase_conf.get("initial", "use_initial_alignment")
if use_initial and (use_initial is None or use_initial_alg == ''):
raise RuntimeError("Using which initial alignment? \n \
set use_initial_alignment in the config file.")
def is_alignment_available(alg):
return alg.startswith(INITIAL_PREF)
def is_data_available(code):
return len(names) > code and names[code] != ""
def get_model_string(ml, ds_name, **kwargs):
def get_model_string(ml,ds_name,**kwargs):
model = (twophase_conf.get("MODELS", "default.model")
if (not twophase_conf.has_option("MODELS","override.default.model.%s" %ds_name)
or twophase_conf.get("MODELS","override.default.model.%s" %ds_name) == '')
else twophase_conf.get("MODELS","override.default.model.%s" %ds_name))
model = (model if not twophase_conf.has_option("MODELS","%s.name.model.%s"%(ml,model))
else twophase_conf.get("MODELS","%s.name.model.%s"%(ml,model)))
dt = twophase_conf.get("MODELS", "default.DT")
dt = (dt if not twophase_conf.has_option("MODELS","%s.name.DT.%s"%(ml,dt))
else twophase_conf.get("MODELS","%s.name.DT.%s"%(ml,dt)))
g = (twophase_conf.get("MODELS", "default.G") if not kwargs.has_key("g")
else kwargs["g"])
g = (g if not twophase_conf.has_option("MODELS","%s.name.G.%s"%(ml,g))
else twophase_conf.get("MODELS","%s.name.G.%s"%(ml,g)))
f = twophase_conf.get("MODELS", "default.F")
f = (f if not twophase_conf.has_option("MODELS","%s.name.F.%s"%(ml,f))
else twophase_conf.get("MODELS","%s.name.F.%s"%(ml,f)))
i = twophase_conf.get("MODELS", "default.I")
i = (i if not twophase_conf.has_option("MODELS","%s.name.I.%s"%(ml,i))
else twophase_conf.get("MODELS","%s.name.I.%s"%(ml,i)))
modelString = (twophase_conf.get("MODELS", "%s.pattern" %ml).format(DT=dt,
G=g,
F=f,
I=i,
model=model)
if twophase_conf.has_option("MODELS", "%s.pattern" %ml)
else "")
#print modelString
return modelString
'''
Created on Jul 18, 2011
@author: smirarab
'''
from mirphyl.twophase import datasets, mltools, algtools, CONFPATH,\
twophase_conf
from mirphyl.setup import get_datasets, get_tool_path, HOME
import sys
import os
from shutil import copyfile
from mirphyl.setup.utilities import require_dir
IGNORE_MISSING_OPTIONAL_FILES = twophase_conf.get("default","IGNORE_OPTIONAL_FILES")
config_path = os.path.join(CONFPATH,"config_files")
CODE_SEQ=0
CODE_REFTREE=1
CODE_REFALG=2
DUMMY = "dummy"
ALIGNED = "aligned.fasta"
INPUT="input.fasta"
INITIAL_PREF = "initial."
SPFN_STAT="spfn.stat"
ALG_STAT="alg.stat"
condor_templates_path = os.path.join(CONFPATH,"condor_templates")
condor_temp_def = open(os.path.join(condor_templates_path, "condor.default")).read()
use_initial = twophase_conf.getboolean("initial", "use_initial")
config_path = os.path.join(CONFPATH, "config_files")
CODE_SEQ = 0
CODE_REFTREE = 1
CODE_REFALG = 2
DUMMY = "dummy"
ALIGNED = "aligned.fasta"
INPUT = "input.fasta"
INITIAL_PREF = "initial."
SPFN_STAT = "spfn.stat"
ALG_STAT = "alg.stat"
condor_templates_path = os.path.join(CONFPATH, "condor_templates")
condor_temp_def = open(os.path.join(condor_templates_path,
"condor.default")).read()
use_initial = twophase_conf.getboolean("initial", "use_initial")
use_initial_alg = twophase_conf.get("initial", "use_initial_alignment")
if use_initial and (use_initial is None or use_initial_alg == ''):
raise RuntimeError("Using which initial alignment? \n \
set use_initial_alignment in the config file.")
def is_alignment_available(alg):
return alg.startswith(INITIAL_PREF)
def is_data_available(code):
return len(names) > code and names[code] != ""
def get_model_string(ml, ds_name, **kwargs):
config_path = os.path.join(CONFPATH,"config_files")
CODE_SEQ=0
CODE_REFTREE=1
CODE_REFALG=2
DUMMY = "dummy"
ALIGNED = "aligned.fasta"
INPUT="input.fasta"
INITIAL_PREF = "initial."
SPFN_STAT="spfn.stat"
ALG_STAT="alg.stat"
condor_templates_path = os.path.join(CONFPATH,"condor_templates")
condor_temp_def = open(os.path.join(condor_templates_path, "condor.default")).read()
use_initial = twophase_conf.getboolean("initial", "use_initial")
use_initial_alg = twophase_conf.get("initial", "use_initial_alignment")
if use_initial and (use_initial is None or use_initial_alg == ''):
raise RuntimeError("Using which initial alignment? \n \
set use_initial_alignment in the config file.")
def is_alignment_available (alg):
return alg.startswith(INITIAL_PREF)
def is_data_available(code):
return len(names)>code and names[code] != ""
def get_model_string(ml,ds_name,**kwargs):
model = (twophase_conf.get("MODELS", "default.model")
if (not twophase_conf.has_option("MODELS","override.default.model.%s" %ds_name)
or twophase_conf.get("MODELS","override.default.model.%s" %ds_name) == '')
'''
Created on Jul 18, 2011
@author: smirarab
'''
from mirphyl.twophase import datasets, mltools, algtools, CONFPATH,\
twophase_conf
from mirphyl.setup import get_datasets, get_tool_path, HOME
import sys
import os
from shutil import copyfile
from mirphyl.setup.utilities import require_dir
IGNORE_MISSING_OPTIONAL_FILES = twophase_conf.get("default","IGNORE_OPTIONAL_FILES")
config_path = os.path.join(CONFPATH,"config_files")
CODE_SEQ=0
CODE_REFTREE=1
CODE_REFALG=2
DUMMY = "dummy"
ALIGNED = "aligned.fasta"
INPUT="input.fasta"
INITIAL_PREF = "initial."
SPFN_STAT="spfn.stat"
ALG_STAT="alg.stat"
condor_templates_path = os.path.join(CONFPATH,"condor_templates")
condor_temp_def = open(os.path.join(condor_templates_path, "condor.default")).read()
use_initial = twophase_conf.getboolean("initial", "use_initial")
