def pyevenn(datasets,figurename='defaultevenn.png',outputdir=''):
outputdir=os.path.abspath(outputdir)
if not os.path.exists(os.path.join(outputdir,'evenn')):
os.mkdir(os.path.join(outputdir,'evenn'))
os.mkdir(os.path.join(outputdir,'evenn','input'))
os.mkdir(os.path.join(outputdir,'evenn','output'))
else:
fhutils.execwrapper('rm -r '+os.path.join(outputdir,'evenn'))
os.mkdir(os.path.join(outputdir,'evenn'))
os.mkdir(os.path.join(outputdir,'evenn','input'))
os.mkdir(os.path.join(outputdir,'evenn','output'))
inputdir=os.path.join(outputdir,'evenn','input')
print inputdir
outputdir=os.path.join(outputdir,'evenn','output')
tabnames = writesets(datasets,outputdir=inputdir,outformat='evenn')
nomvector=robjects.vectors.StrVector(tabnames)
robjects.r("rm(list = ls()); graphics.off()")
robjects.r("""pathnames <- list.files(pattern="[.]R$", path=Sys.getenv('FHR'), full.names=TRUE)""")
robjects.r("sapply(pathnames, FUN=source)")
fh_evenn=robjects.r("fh_evenn")
fh_evenn(inputdir,nomvector,outputdir)
files=os.listdir(outputdir)
for folder in files:
if os.path.isdir(os.path.join(outputdir,folder)):
vennout=os.listdir(os.path.join(outputdir,folder))
for fi in vennout:
if fi=='venn_diagram.png':
fi=os.path.join(outputdir,folder,'venn_diagram.png')
os.rename(fi,figurename)
def pyevenn(datasets, figurename='defaultevenn.png', outputdir=''):
outputdir = os.path.abspath(outputdir)
if not os.path.exists(os.path.join(outputdir, 'evenn')):
os.mkdir(os.path.join(outputdir, 'evenn'))
os.mkdir(os.path.join(outputdir, 'evenn', 'input'))
os.mkdir(os.path.join(outputdir, 'evenn', 'output'))
else:
fhutils.execwrapper('rm -r ' + os.path.join(outputdir, 'evenn'))
os.mkdir(os.path.join(outputdir, 'evenn'))
os.mkdir(os.path.join(outputdir, 'evenn', 'input'))
os.mkdir(os.path.join(outputdir, 'evenn', 'output'))
inputdir = os.path.join(outputdir, 'evenn', 'input')
print inputdir
outputdir = os.path.join(outputdir, 'evenn', 'output')
tabnames = writesets(datasets, outputdir=inputdir, outformat='evenn')
nomvector = robjects.vectors.StrVector(tabnames)
robjects.r("rm(list = ls()); graphics.off()")
robjects.r(
"""pathnames <- list.files(pattern="[.]R$", path=Sys.getenv('FHR'), full.names=TRUE)"""
)
robjects.r("sapply(pathnames, FUN=source)")
fh_evenn = robjects.r("fh_evenn")
fh_evenn(inputdir, nomvector, outputdir)
files = os.listdir(outputdir)
for folder in files:
if os.path.isdir(os.path.join(outputdir, folder)):
vennout = os.listdir(os.path.join(outputdir, folder))
for fi in vennout:
if fi == 'venn_diagram.png':
fi = os.path.join(outputdir, folder, 'venn_diagram.png')
os.rename(fi, figurename)
def rrunner(scriptstring,clean=False):
"""help function if no rpy is available - now disabled """
scriptfile=str(os.getpid())+'execute.R'
out=open(scriptfile,'w')
out.write(scriptstring)
out.close()
command ='R CMD BATCH --no-restore --slave --no-save '+scriptfile
ret=fhutils.execwrapper(command)
if ret == 0 and clean == True:
os.remove(scriptfile)
os.remove(scriptfile+'out')
else:
os.rename(scriptfile,scriptfile+str(fhutils.dtk()))
os.rename(scriptfile+'out',scriptfile+'.out'+str(fhutils.dtk()))
def rrunner(scriptstring, clean=False):
"""help function if no rpy is available - now disabled """
scriptfile = str(os.getpid()) + 'execute.R'
out = open(scriptfile, 'w')
out.write(scriptstring)
out.close()
command = 'R CMD BATCH --no-restore --slave --no-save ' + scriptfile
ret = fhutils.execwrapper(command)
if ret == 0 and clean == True:
os.remove(scriptfile)
os.remove(scriptfile + 'out')
else:
os.rename(scriptfile, scriptfile + str(fhutils.dtk()))
os.rename(scriptfile + 'out', scriptfile + '.out' + str(fhutils.dtk()))
def rrunner(scriptstring, datafile, clean=True):
scriptfile = str(os.getpid()) + 'execute.R'
out = open(scriptfile, 'w')
out.write(scriptstring)
out.close()
command = 'R CMD BATCH --no-restore --slave --no-save ' + scriptfile
ret = fhutils.execwrapper(command)
if ret == 0:
if datafile:
os.remove(datafile)
os.remove(scriptfile)
os.remove(scriptfile + 'out')
else:
if datafile:
os.rename(datafile, datafile + str(fhutils.dtk()))
os.rename(scriptfile, scriptfile + str(fhutils.dtk()))
os.rename(scriptfile + 'out', scriptfile + '.out' + str(fhutils.dtk()))