def getRunStatement(self, infile, outfile, controlfile):
"""
Generate a specific run statement for each peakcaller class
"""
# select location of the spp script to run
if self.PARAMS_PEAKCALLER["spp_options_idr_script"] == "default":
executable = P.which("run_spp.R")
elif self.PARAMS_PEAKCALLER["spp_options_idr_script"] == "nodups":
executable = P.which("run_spp_nodups.R")
else:
executable = self.PARAMS_PEAKCALLER["spp_options_idr_script"]
try:
os.path.exists(executable)
except:
raise IOError("SPP script not found: %s" % executable)
# select the threshold for lax peak calling
if self.PARAMS_PEAKCALLER["spp_options_npeaks"]:
if self.PARAMS_PEAKCALLER["spp_options_fdr"]:
raise Exception("Value specified for both SPP options"
" -npeaks and -fdr please select one or"
" other option, but not both")
else:
threshold = "-npeaks=" + \
str(self.PARAMS_PEAKCALLER["spp_options_npeaks"])
elif self.PARAMS_PEAKCALLER["spp_options_fdr"]:
threshold = "-fdr=" + \
str(self.PARAMS_PEAKCALLER["spp_options_fdr"])
else:
raise Exception("Must specify a value for either"
" spp_options_npeaks or spp_options_fdr,"
" but not both")
# build run statement for spp.
# -savn is output.npeak.file (passed as NULL,
# means filename based on infile)
# -out is output.result.file
# -odir defaults to os.path.dirname( infile )
# -savn is save narrowpeak file
# -savr is save regionpeak file
# (run_spp.R script throws an error if region peak is not output).
statement = [("Rscript %(executable)s"
" -c=%(infile)s"
" -i=%(controlfile)s"
" %(threshold)s"
" -savn"
" -savr")]
# add additional options
statement.append(self.PARAMS_PEAKCALLER["spp_options_parameters"])
# specify outfile
statement.append(" -rf"
" -out=/stats/phantomPeakStatsReps.tab"
" >& %(outfile)s")
statement = (" ".join(statement) % locals())
return statement
def getRunStatement(self, infile, outfile, controlfile):
"""
Generate a specific run statement for each peakcaller class
"""
# select location of the spp script to run
if self.PARAMS_PEAKCALLER["spp_options_idr_script"] == "default":
executable = P.which("run_spp.R")
elif self.PARAMS_PEAKCALLER["spp_options_idr_script"] == "nodups":
executable = P.which("run_spp_nodups.R")
else:
executable = self.PARAMS_PEAKCALLER["spp_options_idr_script"]
try:
os.path.exists(executable)
except:
raise IOError("SPP script not found: %s" % executable)
# select the threshold for lax peak calling
if self.PARAMS_PEAKCALLER["spp_options_npeaks"]:
if self.PARAMS_PEAKCALLER["spp_options_fdr"]:
raise Exception("Value specified for both SPP options"
" -npeaks and -fdr please select one or"
" other option, but not both")
else:
threshold = "-npeaks=" + \
str(self.PARAMS_PEAKCALLER["spp_options_npeaks"])
elif self.PARAMS_PEAKCALLER["spp_options_fdr"]:
threshold = "-fdr=" + \
str(self.PARAMS_PEAKCALLER["spp_options_fdr"])
else:
raise Exception("Must specify a value for either"
" spp_options_npeaks or spp_options_fdr,"
" but not both")
# build run statement for spp.
# -savn is output.npeak.file (passed as NULL,
# means filename based on infile)
# -out is output.result.file
# -odir defaults to os.path.dirname( infile )
# -savn is save narrowpeak file
# -savr is save regionpeak file
# (run_spp.R script throws an error if region peak is not output).
statement = [("Rscript %(executable)s"
" -c=%(infile)s"
" -i=%(controlfile)s"
" %(threshold)s"
" -savn"
" -savr")]
# add additional options
statement.append(self.PARAMS_PEAKCALLER["spp_options_parameters"])
# specify outfile
statement.append(" -rf"
" -out=/stats/phantomPeakStatsReps.tab"
" >& %(outfile)s")
statement = (" ".join(statement) % locals())
return statement
def runControlCPC(infile, outfile):
# farm.py is called from within cpc.sh
assert P.which("farm.py"), "farm.py needs to be in $PATH for cpc to run"
# Default cpc parameters don't work with later versions of blast
E.info("Running cpc with blast version:%s" % P.which("blastx"))
result_evidence = P.snip(outfile, ".result") + ".evidence"
working_dir = "lncRNA_control/cpc"
statement = ("%(scriptsdir)s/cpc.sh"
" %(infile)s"
" %(outfile)s"
" %(working_dir)s"
" %(result_evidence)s")
P.run()
def runControlCPC(infile, outfile):
# farm.py is called from within cpc.sh
assert P.which("farm.py"), "farm.py needs to be in $PATH for cpc to run"
# Default cpc parameters don't work with later versions of blast
E.info("Running cpc with blast version:%s" % P.which("blastx"))
result_evidence = P.snip(outfile, ".result") + ".evidence"
working_dir = "lncRNA_control/cpc"
statement = ("%(scriptsdir)s/cpc.sh"
" %(infile)s"
" %(outfile)s"
" %(working_dir)s"
" %(result_evidence)s")
P.run()