def __init__(self, biodb_selector, fam_path, index_col= "Name", calculation_type="sum"):
self.biodb_selector= biodb_selector
self.abundance_frame= read_csv(fam_path, sep= '\t', index_col=index_col)
self.abundance= self.abundance_frame.T.mean()
self.assembler= Assembler(biodb_selector, self.abundance, calculation_type)
self.assembler.assemble_ideograms()
self.io_worker= IOWorker(self.assembler)
class InputBuilder(object):
def __init__(self, biodb_selector, fam_path, index_col= "Name", calculation_type="sum"):
self.biodb_selector= biodb_selector
self.abundance_frame= read_csv(fam_path, sep= '\t', index_col=index_col)
self.abundance= self.abundance_frame.T.mean()
self.assembler= Assembler(biodb_selector, self.abundance, calculation_type)
self.assembler.assemble_ideograms()
self.io_worker= IOWorker(self.assembler)
def build_circos_inputs_and_run(self, plots=None, links=None, highlights=None):
"""
pathway names will be added
"""
self.io_worker.build_links(links)
self.io_worker.build_highlights(highlights)
self.io_worker.edit_plots_config(plots)
self.io_worker.build_karyotype()
self.io_worker.build_text()
self.io_worker.build_pathway_names()
self.io_worker.build_data()
self.save_settings(plots, links, highlights)
self.run_circos()
def save_settings(self, plots, links, highlights):
plots.dump()
links.dump()
highlights.dump()
def run_circos(self):
circos_file= file_provider['output']['circos_png']
config= file_provider['circos_config']['conf']
out_dir = os.path.dirname(circos_file)
out_file= os.path.basename(circos_file)
circos_bin= file_provider['circos']['bin']
cmd_args= ['perl', circos_bin,'--conf', config,' --outputdir', out_dir, '--outputfile', out_file]
cmd= ' '.join(cmd_args)
print "Running circos...", cmd
p= subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr= subprocess.PIPE)
#p= subprocess.Popen(cmd_args)
output, err= p.communicate()
print output
print "#####"
print err
return output
def build_optionals(self):
pass