input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak.gz", name="CTCF") params.ctcf_reader.read_file() # set path to the CTCF_orient file: params.ctcf_reader.set_sites_orientation( input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak-orient.bed" ) if params.keep_only_orient: params.ctcf_reader.keep_only_with_orient_data() # set corresponding predictor generators and its options: OrientCtcfpg = SitesOrientPredictorGenerator(params.ctcf_reader, N_closest=4) NotOrientCTCFpg = SmallChipSeqPredictorGenerator(params.ctcf_reader, params.window_size, N_closest=4) # Read CTCF data and drop sites w/o known orientation params.ctcf_reader_orientOnly = ChiPSeqReader( input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak.gz", name="CTCF") params.ctcf_reader_orientOnly.read_file() params.ctcf_reader_orientOnly.set_sites_orientation( input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak-orient.bed" ) params.ctcf_reader_orientOnly.keep_only_with_orient_data() # set corresponding predictor generators and its options: OrientBlocksCTCFpg = OrientBlocksPredictorGenerator(
params.contacts_reader.delete_region(deletion) # Read CTCF data logging.info('create CTCF_PG') params.ctcf_reader = ChiPSeqReader(input_folder + "/" + cell_type + "/CTCF/" + CTCF_file_name, name="CTCF") params.ctcf_reader.read_file() #params.ctcf_reader.set_sites_orientation(input_folder +"/"+ cell_type+"/CTCF/"+CTCF_file_name+"-orient.bed") if params.keep_only_orient: params.ctcf_reader.keep_only_with_orient_data() if rearrangement: params.ctcf_reader.delete_region(deletion) OrientCtcfpg = SitesOrientPredictorGenerator(params.ctcf_reader, N_closest=4) NotOrientCTCFpg = SmallChipSeqPredictorGenerator(params.ctcf_reader, params.binsize, N_closest=4) ConvergentPairPG = ConvergentPairPredictorGenerator(params.ctcf_reader, binsize=params.binsize) # Read CTCF data and drop sites w/o known orientation # params.ctcf_reader_orientOnly = ChiPSeqReader(input_folder+"/" + cell_type+"/CTCF/"+CTCF_file_name,name="CTCF") # params.ctcf_reader_orientOnly.read_file() # params.ctcf_reader_orientOnly.set_sites_orientation(input_folder + "/" + cell_type+"/CTCF/"+CTCF_file_name+"-orient.bed") # params.ctcf_reader_orientOnly.keep_only_with_orient_data() if rearrangement: params.ctcf_reader_orientOnly.delete_region(deletion) OrientBlocksCTCFpg = OrientBlocksPredictorGenerator( params.ctcf_reader_orientOnly, params.binsize)
# loopspg = loopsPredictorGenerator(loopsReader, params.window_size) # Read CTCF data logging.info('create CTCF_PG') params.ctcf_reader = ChiPSeqReader(input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak.gz", name="CTCF") params.ctcf_reader.read_file() params.ctcf_reader.set_sites_orientation( input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak-orient.bed") if params.keep_only_orient: params.ctcf_reader.keep_only_with_orient_data() OrientCtcfpg = SitesOrientPredictorGenerator(params.ctcf_reader, N_closest=4) NotOrientCTCFpg = SmallChipSeqPredictorGenerator(params.ctcf_reader, params.window_size, N_closest=4) # Read CTCF data and drop sites w/o known orientation params.ctcf_reader_orientOnly = ChiPSeqReader(input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak.gz", name="CTCF") params.ctcf_reader_orientOnly.read_file() params.ctcf_reader_orientOnly.set_sites_orientation( input_folder + "CTCF/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak-orient.bed") params.ctcf_reader_orientOnly.keep_only_with_orient_data() OrientBlocksCTCFpg = OrientBlocksPredictorGenerator(params.ctcf_reader_orientOnly, params.window_size) ConvergentPairPG = ConvergentPairPredictorGenerator(params.ctcf_reader, binsize=params.window_size) #Read other chip-seq data logging.info('create chipPG')
# Read CTCF data logging.info('create CTCF_PG') params.ctcf_reader = ChiPSeqReader( input_folder + "H1/CTCF/CTCF_H1_conservative_peaks.bed.gz", name="CTCF") params.ctcf_reader.read_file() params.ctcf_reader.set_sites_orientation( input_folder + "H1/CTCF/CTCF_H1_conservative_peaks_orient.bed") if params.keep_only_orient: params.ctcf_reader.keep_only_with_orient_data() OrientCtcfpg = SitesOrientPredictorGenerator(params.ctcf_reader, N_closest=4) NotOrientCTCFpg = SmallChipSeqPredictorGenerator(params.ctcf_reader, params.window_size, N_closest=4) # Read CTCF data and drop sites w/o known orientation params.ctcf_reader_orientOnly = ChiPSeqReader( input_folder + "H1/CTCF/CTCF_H1_conservative_peaks.bed.gz", name="CTCF") params.ctcf_reader_orientOnly.read_file() params.ctcf_reader_orientOnly.set_sites_orientation( input_folder + "H1/CTCF/CTCF_H1_conservative_peaks_orient.bed") params.ctcf_reader_orientOnly.keep_only_with_orient_data() OrientBlocksCTCFpg = OrientBlocksPredictorGenerator( params.ctcf_reader_orientOnly, params.window_size) ConvergentPairPG = ConvergentPairPredictorGenerator( params.ctcf_reader, binsize=params.window_size)