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)