def __init__(self,*filenames,**kwargs): #data_format=None,printer=None):
"""Create a |BigBedGenomeHash|
Parameters
----------
filenames : str or list of str
Filename or list of filenames of `Tabix`_-compressed files
data_format : str
Format of tabix-compressed file(s). Choices are:
`'GTF2'`,`'GFF3'`,`'BED'`,`'PSL'` (Default: `GTF2`)
"""
from pysam import Tabixfile
if len(filenames) == 1 and isinstance(filenames[0],list):
filenames = filenames[0]
self.filenames = list(multiopen(filenames))
self.printer = kwargs.get("printer",NullWriter())
data_format = kwargs.get("data_format","GTF2")
try:
self._reader_class = TabixGenomeHash._READERS[data_format]
except ValueError:
msg = "Supported file formats for TabixGenomeHash are: %s" % ", ".join(sorted(TabixGenomeHash._READERS.keys()))
self.printer.write(msg)
raise ValueError(msg)
self.tabix_readers = [Tabixfile(X) for X in self.filenames]
def __init__(self, *filenames, **kwargs): #data_format=None,printer=None):
"""Create a |BigBedGenomeHash|
Parameters
----------
filenames : str or list of str
Filename or list of filenames of `Tabix`_-compressed files
data_format : str
Format of tabix-compressed file(s). Choices are:
`'GTF2'`,`'GFF3'`,`'BED'`,`'PSL'` (Default: `GTF2`)
"""
from pysam import Tabixfile
if len(filenames) == 1 and isinstance(filenames[0], list):
filenames = filenames[0]
self.filenames = list(multiopen(filenames))
self.printer = kwargs.get("printer", NullWriter())
data_format = kwargs.get("data_format", "GTF2")
try:
self._reader_class = TabixGenomeHash._READERS[data_format]
except ValueError:
msg = "Supported file formats for TabixGenomeHash are: %s" % ", ".join(
sorted(TabixGenomeHash._READERS.keys()))
self.printer.write(msg)
raise ValueError(msg)
self.tabix_readers = [Tabixfile(X) for X in self.filenames]
def __init__(
self, *filenames, **kwargs
): #,base_record_format="III",return_type=None,cache_depth=5):
"""Create a |BigBedGenomeHash|
Parameters
----------
*filenames : str
One or more filenames to open (NOT open filehandles)
return_type : class implementing a :py:meth:`from_bed` method
Class of object to return (Default: |SegmentChain|)
"""
from plastid.readers.bigbed import BigBedReader
return_type = kwargs.get("return_type", SegmentChain)
filenames = list(multiopen(filenames))
for filename in filenames:
if not isinstance(filename, str):
raise ValueError("`filename` must be a 'str'. Found a '%s'." %
type(filename))
self.filenames = filenames
self.bigbedreaders = [
BigBedReader(X, return_type=return_type) for X in filenames
]
def __init__(self, *streams, **kwargs):
"""
AssembledFeatureReader(*streams, return_type=SegmentChain, add_three_for_stop=False, printer=None, tabix=False, **kwargs)
Parameters
----------
streams : file-like
One or more fileneames or open filehandles of input data.
return_type : |SegmentChain| or subclass, optional
Type of feature to return from assembled subfeatures (Default: |SegmentChain|)
add_three_for_stop : bool, optional
Some annotation files exclude the stop codon from CDS annotations. If set to
`True`, three nucleotides will be added to the threeprime end of each
CDS annotation, **UNLESS** the annotated transcript contains explicit stop_codon
feature. (Default: `False`)
printer : file-like, optional
Logger implementing a ``write()`` method. Default: |NullWriter|
tabix : boolean, optional
`streams` point to `tabix`_-compressed files or are open
:class:`~pysam.ctabix.tabix_file_iterator` (Default: `False`)
**kwargs
Other keyword arguments used by specific parsers
"""
streams = multiopen(streams, fn=open, kwargs=dict(mode="rb"))
if kwargs.get("tabix", False) == True:
self.stream = itertools.chain.from_iterable(
(_tabix_iteradaptor(X) for X in streams))
else:
self.stream = itertools.chain.from_iterable(streams)
self.counter = 0
self.printer = kwargs.get("printer", NullWriter())
self.return_type = kwargs.get("return_type", SegmentChain)
add_three_for_stop = kwargs.get("add_three_for_stop", False)
self._finalize = add_three_for_stop_codon if add_three_for_stop == True else lambda x: x
self.metadata = {}
self.rejected = []
def __init__(self,*streams,**kwargs):
"""
AssembledFeatureReader(*streams, return_type=SegmentChain, add_three_for_stop=False, printer=None, tabix=False, **kwargs)
Parameters
----------
streams : file-like
One or more fileneames or open filehandles of input data.
return_type : |SegmentChain| or subclass, optional
Type of feature to return from assembled subfeatures (Default: |SegmentChain|)
add_three_for_stop : bool, optional
Some annotation files exclude the stop codon from CDS annotations. If set to
`True`, three nucleotides will be added to the threeprime end of each
CDS annotation, **UNLESS** the annotated transcript contains explicit stop_codon
feature. (Default: `False`)
printer : file-like, optional
Logger implementing a ``write()`` method. Default: |NullWriter|
tabix : boolean, optional
`streams` point to `tabix`_-compressed files or are open
:class:`~pysam.ctabix.tabix_file_iterator` (Default: `False`)
**kwargs
Other keyword arguments used by specific parsers
"""
streams = multiopen(streams,fn=open,kwargs=dict(mode="rb"))
if kwargs.get("tabix",False) == True:
self.stream = itertools.chain.from_iterable((_tabix_iteradaptor(X) for X in streams))
else:
self.stream = itertools.chain.from_iterable(streams)
self.counter = 0
self.printer = kwargs.get("printer",NullWriter())
self.return_type = kwargs.get("return_type",SegmentChain)
add_three_for_stop = kwargs.get("add_three_for_stop",False)
self._finalize = add_three_for_stop_codon if add_three_for_stop == True else lambda x: x
self.metadata = {}
self.rejected = []
def __init__(self,*filenames,**kwargs): #,base_record_format="III",return_type=None,cache_depth=5):
"""Create a |BigBedGenomeHash|
Parameters
----------
*filenames : str
One or more filenames to open (NOT open filehandles)
return_type : class implementing a :py:meth:`from_bed` method
Class of object to return (Default: |SegmentChain|)
"""
from plastid.readers.bigbed import BigBedReader
return_type = kwargs.get("return_type",SegmentChain)
filenames = list(multiopen(filenames))
for filename in filenames:
if not isinstance(filename,str):
raise ValueError("`filename` must be a 'str'. Found a '%s'." % type(filename))
self.filenames = filenames
self.bigbedreaders = [BigBedReader(X,return_type=return_type) for X in filenames]