def callpeaks(self, peakscaller, controlsample=None, name=None):
'''
This will call the peak caller of choice on selected lane.
:param peakscaller:
:param controlsample:
:param name:
:return:
'''
if not hasattr(peakscaller, 'run_peakcaller'):
raise AttributeError(
'First parameter to call peaks should be a peak caller and %s was missing %s'
% (peakscaller, 'run_peakcaller')
)
temp_dir = os.path.join(self.lane.base_path, 'cache', peakscaller.peakcaller_name, name)
alignment.commons.ensure_path(temp_dir)
peakscaller.run_peakcaller(self, controlsample, temp_dir)
#print(temp_dir)
res = peakscaller.load_peaks(temp_dir)
annotation = annotate.AnnotatePeaks(res, self.genome.data_path)
anno_peaks = annotation.call_me()
if name is None:
name = self.name + '_peaks_' + peakscaller.peakcaller_name
if controlsample:
name += '_vs_' + controlsample.name
peak_file_path = os.path.join(self.lane.base_path, 'results', 'Peaks', name)
alignment.commons.ensure_path(peak_file_path)
anno_peaks.to_csv(os.path.join(peak_file_path, name+'.tsv'), sep='\t', header=True, index=False)
