def __init__(self, rec):
"""Constructs a new object with the given fastq record"""
# strip quiver appendage from name
if rec.name.endswith("|quiver"):
self._name = rec.name[:rec.name.index('|quiver')]
else:
self._name = rec.name[:rec.name.index('|arrow')]
self._qv = np.average(rec.quality)
self._len = len(rec.sequence)
self._cov = ContigCoverage(self._name)
class ContigInfo(object):
"""Contains relevant contig information needed for plotting. Contig id,
length and averaged QV and average coverage depth.
"""
def __init__(self, rec):
"""Constructs a new object with the given fastq record"""
# strip quiver appendage from name
if rec.name.endswith("|quiver"):
self._name = rec.name[:rec.name.index('|quiver')]
else:
self._name = rec.name[:rec.name.index('|arrow')]
self._qv = np.average(rec.quality)
self._len = len(rec.sequence)
self._cov = ContigCoverage(self._name)
def __repr__(self):
_d = dict(k=self.__class__.__name__, n=self.name, l=self.length)
return "<{k} name:{n} length:{l} >".format(**_d)
def add_coverage_data(self, gffrec):
"""Adds coverage information from a gff record"""
self._cov.add_data(gffrec)
@property
def name(self):
"""Contig name (or ID)"""
return self._name
@property
def mean_qv(self):
"""Mean QV value"""
return self._qv
@property
def length(self):
"""Contig length"""
return self._len
@property
def mean_coverage(self):
"""Mean coverage"""
return self._cov.meanCoveragePerBase()
def __init__(self, rec):
"""Constructs a new object with the given fastq record"""
# strip quiver appendage from name
if rec.name.endswith("|quiver"):
self._name = rec.name[:rec.name.index('|quiver')]
else:
self._name = rec.name[:rec.name.index('|arrow')]
self._qv = np.average(rec.quality)
self._len = len(rec.sequence)
self._cov = ContigCoverage(self._name)
class ContigInfo(object):
"""Contains relevant contig information needed for plotting. Contig id,
length and averaged QV and average coverage depth.
"""
def __init__(self, rec):
"""Constructs a new object with the given fastq record"""
# strip quiver appendage from name
if rec.name.endswith("|quiver"):
self._name = rec.name[:rec.name.index('|quiver')]
else:
self._name = rec.name[:rec.name.index('|arrow')]
self._qv = np.average(rec.quality)
self._len = len(rec.sequence)
self._cov = ContigCoverage(self._name)
def __repr__(self):
_d = dict(k=self.__class__.__name__, n=self.name, l=self.length)
return "<{k} name:{n} length:{l} >".format(**_d)
def add_coverage_data(self, gffrec):
"""Adds coverage information from a gff record"""
self._cov.add_data(gffrec)
@property
def name(self):
"""Contig name (or ID)"""
return self._name
@property
def mean_qv(self):
"""Mean QV value"""
return self._qv
@property
def length(self):
"""Contig length"""
return self._len
@property
def mean_coverage(self):
"""Mean coverage"""
return self._cov.meanCoveragePerBase()