def __init__(self, samples, prefix, output_prefix, dependencies=()):
abs_prefix = os.path.abspath(prefix)
script = rtools.rscript("zonkey", "pca.r")
call = [
"Rscript", script, abs_prefix, "%(IN_SAMPLES)s",
"%(TEMP_OUT_PREFIX)s"
]
cmd = AtomicCmd(call,
AUX_SCRIPT=script,
IN_FILE_EVAL=prefix + ".eval",
IN_FILE_EVEC=prefix + ".evec",
IN_SAMPLES=samples,
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
OUT_PDF=output_prefix + ".pdf",
OUT_PNG=output_prefix + ".png",
CHECK_R=RSCRIPT_VERSION,
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_R_LABELS=rtools.requirement("ggrepel"),
set_cwd=True)
CommandNode.__init__(self,
description="<PlotPCA -> '%s.*'>" %
(output_prefix, ),
command=cmd,
dependencies=dependencies)
def __init__(self,
input_file,
output_prefix,
order,
samples,
dependencies=()):
self._samples = samples
self._order = tuple(order) + ("Sample", )
script = rtools.rscript("zonkey", "admixture.r")
cmd = AtomicCmd(("Rscript", script, "%(IN_FILE)s",
"%(TEMP_OUT_NAMES)s", "%(TEMP_OUT_PREFIX)s"),
AUX_RSCRIPT=script,
IN_FILE=input_file,
IN_SAMPLES=samples,
OUT_PDF=output_prefix + ".pdf",
OUT_PNG=output_prefix + ".png",
TEMP_OUT_NAMES="samples.txt",
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
CHECK_R=RSCRIPT_VERSION,
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_R_RESHAPE2=rtools.requirement("reshape2"),
set_cwd=True)
CommandNode.__init__(self,
description="<AdmixturePlot -> '%s.*'>" %
(output_prefix, ),
command=cmd,
dependencies=dependencies)
def __init__(self, samples, prefix, output_prefix, dependencies=()):
abs_prefix = os.path.abspath(prefix)
script = rtools.rscript("zonkey", "pca.r")
call = ["Rscript", script,
abs_prefix, "%(IN_SAMPLES)s", "%(TEMP_OUT_PREFIX)s"]
cmd = AtomicCmd(call,
AUX_SCRIPT=script,
IN_FILE_EVAL=prefix + ".eval",
IN_FILE_EVEC=prefix + ".evec",
IN_SAMPLES=samples,
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
OUT_PDF=output_prefix + ".pdf",
OUT_PNG=output_prefix + ".png",
CHECK_R=RSCRIPT_VERSION,
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_R_LABELS=rtools.requirement("directlabels"),
set_cwd=True)
CommandNode.__init__(self,
description="<PlotPCA -> '%s.*'>"
% (output_prefix,),
command=cmd,
dependencies=dependencies)
def __init__(self, input_file, output_prefix, order, samples,
dependencies=()):
self._samples = samples
self._order = tuple(order) + ("Sample",)
script = rtools.rscript("zonkey", "admixture.r")
cmd = AtomicCmd(("Rscript", script, "%(IN_FILE)s",
"%(TEMP_OUT_NAMES)s", "%(TEMP_OUT_PREFIX)s"),
AUX_RSCRIPT=script,
IN_FILE=input_file,
IN_SAMPLES=samples,
OUT_PDF=output_prefix + ".pdf",
OUT_PNG=output_prefix + ".png",
TEMP_OUT_NAMES="samples.txt",
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
CHECK_R=RSCRIPT_VERSION,
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_R_RESHAPE2=rtools.requirement("reshape2"),
set_cwd=True)
CommandNode.__init__(self,
description="<AdmixturePlot -> '%s.*'>"
% (output_prefix,),
command=cmd,
dependencies=dependencies)
def customize(self, reference, directory, dependencies=()):
command = AtomicCmdBuilder(
[
"mapDamage", "--stats-only", "-r", "%(IN_REFERENCE)s", "-d",
"%(TEMP_DIR)s"
],
IN_REFERENCE=reference,
TEMP_OUT_FREQ_3p="3pGtoA_freq.txt",
TEMP_OUT_FREQ_5p="5pCtoT_freq.txt",
TEMP_OUT_COMP_USER="******",
TEMP_OUT_MISINCORP="misincorporation.txt",
TEMP_OUT_LOG="Runtime_log.txt",
TEMP_OUT_STDOUT="pipe_mapDamage.stdout",
TEMP_OUT_STDERR="pipe_mapDamage.stderr",
OUT_COMP_GENOME=os.path.join(directory, "dnacomp_genome.csv"),
OUT_MCMC_PROBS=os.path.join(directory,
"Stats_out_MCMC_correct_prob.csv"),
OUT_MCMC_HIST=os.path.join(directory, "Stats_out_MCMC_hist.pdf"),
OUT_MCMC_ITER=os.path.join(directory, "Stats_out_MCMC_iter.csv"),
OUT_MCMC_ITERSUM=os.path.join(directory,
"Stats_out_MCMC_iter_summ_stat.csv"),
OUT_MCMC_POSTPRED=os.path.join(directory,
"Stats_out_MCMC_post_pred.pdf"),
OUT_MCMC_TRACE=os.path.join(directory, "Stats_out_MCMC_trace.pdf"),
CHECK_RSCRIPT=RSCRIPT_VERSION,
CHECK_MAPDAMAGE=MAPDAMAGE_VERSION,
CHECK_R_INLINE=rtools.requirement("inline"),
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_R_RCPP=rtools.requirement("Rcpp"),
CHECK_R_GAM=rtools.requirement("gam"),
CHECK_R_RCPPGSL=rtools.requirement("RcppGSL"))
return {"command": command, "dependencies": dependencies}
def __init__(self, samples, treefile, bootstraps, output_prefix,
dependencies=()):
rscript = rtools.rscript("zonkey", "tinytree.r")
cmd = AtomicCmd(("Rscript", rscript,
"%(TEMP_OUT_FILE)s",
"%(IN_SAMPLES)s",
"%(TEMP_OUT_PREFIX)s"),
AUX_RSCRIPT=rscript,
IN_SAMPLES=samples,
IN_FILE=treefile,
IN_BOOTSTRAPS=bootstraps,
TEMP_OUT_FILE="rerooted.newick",
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
OUT_TREE_PDF=output_prefix + ".pdf",
OUT_TREE_PNG=output_prefix + ".png",
CHECK_RSCRIPT=RSCRIPT_VERSION,
CHECK_RSCRIPT_APE=rtools.requirement("ape"),
CHECK_RSCRIPT_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_RSCRIPT_GRID=rtools.requirement("grid"))
self._treefile = treefile
self._bootstraps = bootstraps
CommandNode.__init__(self,
description="<DrawPhylogeny -> '%s.*'>"
% (output_prefix,),
command=cmd,
dependencies=dependencies)
def customize(self, reference, directory, dependencies=()):
command = AtomicCmdBuilder(
["mapDamage", "--stats-only",
"-r", "%(IN_REFERENCE)s",
"-d", "%(TEMP_DIR)s"],
IN_REFERENCE=reference,
TEMP_OUT_FREQ_3p="3pGtoA_freq.txt",
TEMP_OUT_FREQ_5p="5pCtoT_freq.txt",
TEMP_OUT_COMP_USER="******",
TEMP_OUT_MISINCORP="misincorporation.txt",
TEMP_OUT_LOG="Runtime_log.txt",
TEMP_OUT_STDOUT="pipe_mapDamage.stdout",
TEMP_OUT_STDERR="pipe_mapDamage.stderr",
OUT_COMP_GENOME=os.path.join(directory, "dnacomp_genome.csv"),
OUT_MCMC_PROBS=os.path.join(directory,
"Stats_out_MCMC_correct_prob.csv"),
OUT_MCMC_HIST=os.path.join(directory, "Stats_out_MCMC_hist.pdf"),
OUT_MCMC_ITER=os.path.join(directory, "Stats_out_MCMC_iter.csv"),
OUT_MCMC_ITERSUM=os.path.join(directory,
"Stats_out_MCMC_iter_summ_stat.csv"),
OUT_MCMC_POSTPRED=os.path.join(directory,
"Stats_out_MCMC_post_pred.pdf"),
OUT_MCMC_TRACE=os.path.join(directory, "Stats_out_MCMC_trace.pdf"),
CHECK_RSCRIPT=RSCRIPT_VERSION,
CHECK_MAPDAMAGE=MAPDAMAGE_VERSION,
CHECK_R_INLINE=rtools.requirement("inline"),
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_R_RCPP=rtools.requirement("Rcpp"),
CHECK_R_GAM=rtools.requirement("gam"),
CHECK_R_RCPPGSL=rtools.requirement("RcppGSL"))
return {"command": command,
"dependencies": dependencies}
def __init__(self,
samples,
treefile,
bootstraps,
output_prefix,
dependencies=()):
rscript = rtools.rscript("zonkey", "tinytree.r")
cmd = AtomicCmd(("Rscript", rscript, "%(TEMP_OUT_FILE)s",
"%(IN_SAMPLES)s", "%(TEMP_OUT_PREFIX)s"),
AUX_RSCRIPT=rscript,
IN_SAMPLES=samples,
IN_FILE=treefile,
IN_BOOTSTRAPS=bootstraps,
TEMP_OUT_FILE="rerooted.newick",
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
OUT_TREE_PDF=output_prefix + ".pdf",
OUT_TREE_PNG=output_prefix + ".png",
CHECK_RSCRIPT=RSCRIPT_VERSION,
CHECK_RSCRIPT_APE=rtools.requirement("ape"),
CHECK_RSCRIPT_GGPLOT2=rtools.requirement("ggplot2"),
CHECK_RSCRIPT_GRID=rtools.requirement("grid"))
self._treefile = treefile
self._bootstraps = bootstraps
CommandNode.__init__(self,
description="<DrawPhylogeny -> '%s.*'>" %
(output_prefix, ),
command=cmd,
dependencies=dependencies)
def __init__(self,
contigs,
mapping,
input_file,
output_prefix,
dependencies=()):
self._contigs = contigs
self._mapping = dict(zip(mapping.values(), mapping))
self._input_file = input_file
script = rtools.rscript("zonkey", "coverage.r")
cmd = AtomicCmd(
("Rscript", script, "%(TEMP_OUT_TABLE)s", "%(TEMP_OUT_PREFIX)s"),
AUX_RSCRIPT=script,
IN_FILE=input_file,
TEMP_OUT_TABLE="contigs.table",
OUT_PDF=output_prefix + ".pdf",
OUT_PNG=output_prefix + ".png",
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
CHECK_R=RSCRIPT_VERSION,
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
set_cwd=True,
)
CommandNode.__init__(
self,
description="<CoveragePlot -> '%s.*'>" % (output_prefix, ),
command=cmd,
dependencies=dependencies,
)
def _plot_command(cls, input_prefix, *args, **kwargs):
script = rtools.rscript("zonkey", "treemix.r")
return AtomicCmd(("Rscript", script) + args,
AUX_RSCRIPT=script,
IN_FILE_COV=input_prefix + ".cov.gz",
IN_FILE_COVSE=input_prefix + ".covse.gz",
IN_FILE_EDGES=input_prefix + ".edges.gz",
IN_FILE_MODELCOV=input_prefix + ".modelcov.gz",
IN_FILE_VERTICES=input_prefix + ".vertices.gz",
CHECK_R=RSCRIPT_VERSION,
CHECK_R_BREW=rtools.requirement("RColorBrewer"),
set_cwd=True,
**kwargs)
def _plot_command(cls, input_prefix, *args, **kwargs):
script = rtools.rscript("zonkey", "treemix.r")
return AtomicCmd(("Rscript", script) + args,
AUX_RSCRIPT=script,
IN_FILE_COV=input_prefix + ".cov.gz",
IN_FILE_COVSE=input_prefix + ".covse.gz",
IN_FILE_EDGES=input_prefix + ".edges.gz",
IN_FILE_MODELCOV=input_prefix + ".modelcov.gz",
IN_FILE_VERTICES=input_prefix + ".vertices.gz",
CHECK_R=RSCRIPT_VERSION,
CHECK_R_BREW=rtools.requirement("RColorBrewer"),
set_cwd=True,
**kwargs)
def __init__(self, contigs, input_file, output_prefix, dependencies=()):
self._contigs = contigs
self._input_file = input_file
script = rtools.rscript("zonkey", "coverage.r")
cmd = AtomicCmd(("Rscript", script,
"%(TEMP_OUT_TABLE)s", "%(TEMP_OUT_PREFIX)s"),
AUX_RSCRIPT=script,
IN_FILE=input_file,
TEMP_OUT_TABLE="contigs.table",
OUT_PDF=output_prefix + ".pdf",
OUT_PNG=output_prefix + ".png",
TEMP_OUT_PREFIX=os.path.basename(output_prefix),
CHECK_R=RSCRIPT_VERSION,
CHECK_R_GGPLOT2=rtools.requirement("ggplot2"),
set_cwd=True)
CommandNode.__init__(self,
description="<CoveragePlot -> '%s.*'>"
% (output_prefix,),
command=cmd,
dependencies=dependencies)
