def main():
rExists = os.system("which r")
if rExists == 256:
print "\n\nYou need to install r first\n\n"
quit()
rscriptExists = os.system("which Rscript")
if rscriptExists == 256:
print "\n\nYou need to install Rscript first\n\n"
quit()
path2files, treesFolder, chromoSizeFile, mappingFile, majorClade, minorsXmajor, majors, criterion, m_interval = get_parameters(
)
# Counting minor clades and filtering by criterion
result_counts = TreesCriteria_counts.count(path2files, treesFolder,
majorClade, mappingFile,
int(criterion))
print "total genes = " + result_counts.split(",")[0]
print "total trees = " + result_counts.split(",")[1]
# Mapping the information
result_mapIntervals = Intervals.mapIntervals(path2files, m_interval,
chromoSizeFile)
print "number of chromosomes: " + str(
result_mapIntervals['number of chromosomes'])
print "map size: " + str(result_mapIntervals['map size'])
print "genes mapped: " + str(result_mapIntervals['genes mapped'])
# Redistributing the loci that are not clearly in an interval.
result_mapInfoHelper = MapInfoHelper.redistributeLoci(path2files)
print result_mapInfoHelper
result_matrix = BuildMapMatrix.BuildMatrix(path2files, minorsXmajor,
majors, m_interval)
os.system("rm *.pyc")
