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_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_spfn_condor_file(outpath):
conv_tool_path = get_tool_path("spfn")
condor_st = condor_temp_def.format(exe=conv_tool_path,
input="-e %s -r reference.fasta" %ALIGNED,
output="-o %s" %SPFN_STAT,
home=HOME,
name="spfn",
options="")
out = open(os.path.join(outpath, "condor.spfn"), "w")
out.write(condor_st)
out.close()
def make_conversion_condor_file(outpath, alg):
conv_tool_path = get_tool_path("readseq")
condor_conv = condor_temp_def.format(exe=conv_tool_path,
options="-f12",
input=INPUT if is_alignment_available(alg) else ALIGNED,
output="-o aligned.phylip",
home=HOME,
name="readseq")
out = open(os.path.join(outpath, "condor.convert"), "w")
out.write(condor_conv)
out.close()
def make_distance_condor_file(outpath):
conv_tool_path = get_tool_path("distance")
condor_st = condor_temp_def.format(exe=conv_tool_path,
input= ALIGNED,
output="distance.stat",
home=HOME,
name="distance",
options="")
out = open(os.path.join(outpath, "condor.distance"), "w")
out.write(condor_st)
out.close()
def make_standardize_condor_file(outpath, alg):
conv_tool_path = get_tool_path("standardizeseqnames")
condor_conv = condor_temp_def.format(exe=conv_tool_path,
options="",
input=INPUT if is_alignment_available(alg) else ALIGNED,
output="aligned.mapped namemap",
home=HOME,
name="standardize")
out = open(os.path.join(outpath, "condor.std"), "w")
out.write(condor_conv)
out.close()
def make_distance_condor_file(outpath):
conv_tool_path = get_tool_path("distance")
condor_st = condor_temp_def.format(exe=conv_tool_path,
input=ALIGNED,
output="distance.stat",
home=HOME,
name="distance",
options="")
out = open(os.path.join(outpath, "condor.distance"), "w")
out.write(condor_st)
out.close()
def make_BS_condor(outpath, num, indir):
tool_path = get_tool_path("multilocus_bootstrap")
condor_conv = condor_temp_def.format(exe=tool_path,
options=num,
input=indir,
output="BS",
home=HOME,
name="rep")
out = open(os.path.join(outpath, "condor.rep"), "w")
out.write(condor_conv)
out.close()
def make_standardize_condor_file(outpath, alg):
conv_tool_path = get_tool_path("standardizeseqnames")
condor_conv = condor_temp_def.format(
exe=conv_tool_path,
options="",
input=INPUT if is_alignment_available(alg) else ALIGNED,
output="aligned.mapped namemap",
home=HOME,
name="standardize")
out = open(os.path.join(outpath, "condor.std"), "w")
out.write(condor_conv)
out.close()
def make_spfn_condor_file(outpath):
conv_tool_path = get_tool_path("spfn")
condor_st = condor_temp_def.format(exe=conv_tool_path,
input="-e %s -r reference.fasta" %
ALIGNED,
output="-o %s" % SPFN_STAT,
home=HOME,
name="spfn",
options="")
out = open(os.path.join(outpath, "condor.spfn"), "w")
out.write(condor_st)
out.close()
def make_map_condor_file(outpath, ml):
conv_tool_path = get_tool_path("mapsequence")
input = 'ml' if not ml.startswith('raxml') else "raxml/RAxML_bipartitions.ml" if ml=="raxmlboot" else 'raxml/RAxML_bestTree.ml'
condor_conv = condor_temp_def.format(exe=conv_tool_path,
options="",
input="%s namemap" %input,
output="ml.mapped -rev",
home=HOME,
name="map")
out = open(os.path.join(outpath, "condor.map"), "w")
out.write(condor_conv)
out.close()
def make_conversion_condor_file(outpath, alg):
conv_tool_path = get_tool_path("readseq")
condor_conv = condor_temp_def.format(
exe=conv_tool_path,
options="-f12",
input=INPUT if is_alignment_available(alg) else ALIGNED,
output="-o aligned.phylip",
home=HOME,
name="readseq")
out = open(os.path.join(outpath, "condor.convert"), "w")
out.write(condor_conv)
out.close()
def make_mbrate_condor_file(outpath,ml):
tool_path = get_tool_path("missingbranch")
input = 'ml'
if ml == 'raxml':
input = 'raxml/RAxML_bestTree.ml'
condor_st = condor_temp_def.format(exe=tool_path,
input="reference.tre %s"%input,
output="mb.stat",
home=HOME,
name="mb",
options="")
out = open(os.path.join(outpath, "condor.mb"), "w")
out.write(condor_st)
out.close()
def make_mbrate_condor_file(outpath, ml):
tool_path = get_tool_path("missingbranch")
input = 'ml'
if ml.startswith('raxml'):
input = 'raxml/RAxML_bestTree.ml'
condor_st = condor_temp_def.format(exe=tool_path,
input="reference.tre %s" % input,
output="mb.stat",
home=HOME,
name="mb",
options="")
out = open(os.path.join(outpath, "condor.mb"), "w")
out.write(condor_st)
out.close()
def make_map_condor_file(outpath, ml):
conv_tool_path = get_tool_path("mapsequence")
input = 'ml' if not ml.startswith(
'raxml'
) else "raxml/RAxML_bipartitions.ml" if ml == "raxmlboot" else 'raxml/RAxML_bestTree.ml'
condor_conv = condor_temp_def.format(exe=conv_tool_path,
options="",
input="%s namemap" % input,
output="ml.mapped -rev",
home=HOME,
name="map")
out = open(os.path.join(outpath, "condor.map"), "w")
out.write(condor_conv)
out.close()
def make_time_condor_files(outpath):
tool_path = get_tool_path("readcondorlog")
condor_st = condor_temp_def.format(exe=tool_path,
input="logs/alg_condor_log",
output= (ALG_STAT if not use_initial else
"%s %s" %(ALG_STAT,"initial_%s"%ALG_STAT)),
home=HOME,
name="rcl",
options="")
out = open(os.path.join(outpath, "condor.read.alg"), "w")
out.write(condor_st)
out.close()
condor_st = condor_temp_def.format(exe=tool_path,
input="logs/ml_condor_log",
output="ml.stat",
home=HOME,
name="rclml",
options="")
out = open(os.path.join(outpath, "condor.read.ml"), "w")
out.write(condor_st)
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 make_time_condor_files(outpath):
tool_path = get_tool_path("readcondorlog")
condor_st = condor_temp_def.format(
exe=tool_path,
input="logs/alg_condor_log",
output=(ALG_STAT if not use_initial else "%s %s" %
(ALG_STAT, "initial_%s" % ALG_STAT)),
home=HOME,
name="rcl",
options="")
out = open(os.path.join(outpath, "condor.read.alg"), "w")
out.write(condor_st)
out.close()
condor_st = condor_temp_def.format(exe=tool_path,
input="logs/ml_condor_log",
output="ml.stat",
home=HOME,
name="rclml",
options="")
out = open(os.path.join(outpath, "condor.read.ml"), "w")
out.write(condor_st)
out.close()
for rep in replicas:
out_rep_path = os.path.join(out_ds_path, "R%d" % rep)
print out_rep_path
require_dir(out_rep_path)
for ml in mltools:
ml_tool = ml.split(".")[0]
for alg in algtools:
out_path = os.path.join(out_rep_path,
"%s_%s" % (ml, alg))
require_dir(out_path)
require_dir(os.path.join(out_path, "logs"))
alg_tool = alg.split(".")[0]
tool_path = get_tool_path("distance")
input = ALIGNED
condor_st = condor_temp_def.format(
exe=tool_path,
input=input,
output="distance.stat",
home=HOME,
name="distance",
options="")
out = open(
os.path.join(out_path, "condor.distance"), "w")
out.write(condor_st)
out.close()
# copy_files_for_replica(ds_path, out_path, rep, names, alg, ds_name)
#
# if not is_alignment_available(alg):
for rep in replicas:
out_rep_path = os.path.join(out_ds_path, "R%d" % rep)
print out_rep_path
require_dir(out_rep_path)
for ml in mltools:
ml_tool = ml.split(".")[0]
for alg in algtools:
out_path = os.path.join(out_rep_path,
"%s_%s" % (ml, alg))
require_dir(out_path)
require_dir(os.path.join(out_path, "logs"))
alg_tool = alg.split(".")[0]
tool_path = get_tool_path("distance")
input = ALIGNED
condor_st = condor_temp_def.format(
exe=tool_path,
input=input,
output="distance.stat",
home=HOME,
name="distance",
options="")
out = open(os.path.join(out_path, "condor.distance"),
"w")
out.write(condor_st)
out.close()
# copy_files_for_replica(ds_path, out_path, rep, names, alg, ds_name)
#
# if not is_alignment_available(alg):
