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): 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 __init__(self, fname): self.fname = fname Model.__init__(self)
def __init__(self, binsize): self.binsize = int(binsize) Model.__init__(self)