def count(self, bam, library_type, coverage=False, uniq_only=False, fpkm=False, norm='', multiple='complete', whitelist=None, blacklist=None, out=sys.stdout, quiet=False, start_only=False):
self.stranded = library_type in ['FR', 'RF']
self.chrom_lens = []
for chrom, chrom_len in zip(bam.references, bam.lengths):
self.chrom_lens.append((chrom, chrom_len))
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm, multiple, whitelist, blacklist, out, quiet, start_only)
def __init__(self, fname=None, fileobj=None):
if fileobj:
self.bed = BedFile(fileobj=fileobj)
self.fname = '*fileobj*'
else:
self.bed = BedFile(fname)
self.fname = fname
Model.__init__(self)
def __init__(self, fname=None, fileobj=None):
if fileobj:
self.bed = BedFile(fileobj=fileobj)
self.fname = '*fileobj*'
else:
self.bed = BedFile(fname)
self.fname = fname
Model.__init__(self)
def __init__(self, fname):
self.fname = fname
Model.__init__(self)
self.gtf = GTF(self.fname)
gene_gen = self.gtf.genes
gene = gene_gen.next()
self.has_isoform = 'isoform_id' in gene.attributes
self.has_biotype = 'gene_biotype' in gene.attributes
def __init__(self, fname):
self.fname = fname
Model.__init__(self)
self.gtf = GTF(self.fname)
gene_gen = self.gtf.genes
gene = gene_gen.next()
self.has_isoform = 'isoform_id' in gene.attributes
self.has_biotype = 'gene_biotype' in gene.attributes
def count(self, bam, library_type, coverage=False, uniq_only=False, fpkm=False, norm='', multiple='complete', whitelist=None, blacklist=None, out=sys.stdout, quiet=False, start_only=False):
self.uniq_only = uniq_only
self.multiple = multiple
self.whitelist = whitelist
self.blacklist = blacklist
self.library_type = library_type
self.stranded = library_type in ['FR', 'RF']
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm, multiple, whitelist, blacklist, out, quiet, start_only)
def count(self,
bam,
library_type,
coverage=False,
uniq_only=False,
fpkm=False,
norm='',
multiple='complete',
whitelist=None,
blacklist=None,
out=sys.stdout,
quiet=False,
start_only=False):
self.stranded = library_type in ['FR', 'RF']
self.chrom_lens = []
for chrom, chrom_len in zip(bam.references, bam.lengths):
self.chrom_lens.append((chrom, chrom_len))
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm,
multiple, whitelist, blacklist, out, quiet, start_only)
def count(self,
bam,
library_type,
coverage=False,
uniq_only=False,
fpkm=False,
norm='',
multiple='complete',
whitelist=None,
blacklist=None,
out=sys.stdout,
quiet=False,
start_only=False):
self.uniq_only = uniq_only
self.multiple = multiple
self.whitelist = whitelist
self.blacklist = blacklist
self.library_type = library_type
self.stranded = library_type in ['FR', 'RF']
Model.count(self, bam, library_type, coverage, uniq_only, fpkm, norm,
multiple, whitelist, blacklist, out, quiet, start_only)
def __init__(self, fname):
self.fname = fname
Model.__init__(self)
def __init__(self, binsize):
self.binsize = int(binsize)
Model.__init__(self)
def __init__(self, fname):
self.fname = fname
Model.__init__(self)
def __init__(self, binsize):
self.binsize = int(binsize)
Model.__init__(self)
