from .RegionParser import RegionParser
from . import COORDS_DEFAULT
from . import TAB, VCF
[docs]class BedParser(RegionParser):
""" Standard Full BED Parser of 10 Columns
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=5,
otherPos=[(3, "3", "string"),
(4, "4", 'double'),
(6, "6", 'double'),
(7, "7", 'double'),
(8, "8", 'double'),
(9, "9", "double")],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
[docs]class ANNParser(RegionParser):
""" Annotation Parser, 6 columns
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=5,
otherPos=[(3, "name", "string"),
(4, "score", 'double')],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
class BroadProjParser(RegionParser):
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=None,
otherPos=[(3, "name", "string")],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
[docs]class BasicParser(RegionParser):
""" Parser for Chr, Start, Stop only (no Strand)
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=None,
otherPos=None,
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
[docs]class NarrowPeakParser(RegionParser):
""" Narrow Peaks Parser. 10 columns
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=5,
otherPos=[(3, "name", "string"),
(4, "score", 'double'),
(6, "signalValue", 'double'),
(7, "pValue", 'double'),
(8, "qValue", 'double'),
(9, "peak", "double")],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
class BroadPeakParser(RegionParser):
""" Broad Peaks Parser. 10 columns
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=5,
otherPos=[(3, "name", "string"),
(4, "score", 'double'),
(6, "signalValue", 'double'),
(7, "pValue", 'double'),
(8, "qValue", 'double')],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
[docs]class RnaSeqParser(RegionParser):
""" Standard Full BED Parser of 10 Columns
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=3,
otherPos=[(4, "name", "string"),
(5, "score", 'double')],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
[docs]class BedScoreParser(RegionParser):
""" Standard Full BED Parser of 10 Columns
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=2,
strandPos=None,
otherPos=[(3, "score", 'double')],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=TAB)
class VCFParser(RegionParser):
""" Parser for VCF files
"""
def __init__(self):
super().__init__(chrPos=0,
startPos=1,
stopPos=1,
otherPos=[(2, "ID", "string"),
(3, "REF", "string"),
(4, "ALT", "string"),
(5, "QUAL", "float"),
(6, "FILTER", "string"),
(7, "INFO", "string"),
(8, "FORMAT", "string")],
delimiter="\t",
coordinate_system=COORDS_DEFAULT,
schema_format=VCF)