def __iter__(self): sf = pysam.Samfile(self.filename, "rb") self.record_no = 0 for pa in sf: try: yield SAM_Alignment.from_pysam_AlignedRead(pa, sf) except OverflowError: pass self.record_no += 1
def __iter__( self ): sf = pysam.Samfile(self.filename, "rb") self.record_no = 0 for pa in sf: try: yield SAM_Alignment.from_pysam_AlignedRead( pa, sf ) except OverflowError: pass self.record_no += 1
def fetch(self, reference=None, start=None, end=None, region=None): sf = pysam.Samfile(self.filename, "rb") self.record_no = 0 try: for pa in sf.fetch(reference, start, end, region): try: yield SAM_Alignment.from_pysam_AlignedRead(pa, sf) except OverflowError: pass self.record_no += 1 except ValueError as e: if e.message == "fetch called on bamfile without index": print "Error: ", e.message print "Your bam index file is missing or wrongly named, convention is that file 'x.bam' has index file 'x.bam.bai'!" else: raise except: raise
def fetch( self, reference = None, start = None, end = None, region = None ): sf = pysam.Samfile(self.filename, "rb") self.record_no = 0 try: for pa in sf.fetch( reference, start, end, region ): try: yield SAM_Alignment.from_pysam_AlignedRead( pa, sf ) except OverflowError: pass self.record_no += 1 except ValueError as e: if e.message == "fetch called on bamfile without index": print "Error: ", e.message print "Your bam index file is missing or wrongly named, convention is that file 'x.bam' has index file 'x.bam.bai'!" else: raise except: raise