MACS3.Signal.UnitigRACollection module

All Parser classes

class MACS3.Signal.UnitigRACollection.UnitigCollection(chrom, peak, URAs_list=[])

Bases: object

A collection of ReadAlignment objects and the corresponding PeakIO.

URAs_left: typedef

URAs_list: list

URAs_right: typedef

chrom: bytes

get_PosReadsInfo_ref_pos(ref_pos, ref_nt, Q=20)

Generate a PosReadsInfo for: object a given reference genome position.

Return a PosReadsInfo object.

is_sorted: _fake_callable

left: typedef

length: typedef

peak: PeakIO

right: typedef

sort(): Sort RAs according to lpos. Should be used after realignment.

class MACS3.Signal.UnitigRACollection.UnitigRAs(chrom, lpos, rpos, unitig_aln, reference_aln, RAlists)

Bases: object

RAlists: list

aln_length: typedef

chrom: bytes

get_variant_bq_by_ref_pos(ref_pos)

return (s, bq_list_t, bq_list_c, strand_list_t, strand_list_c)

Return type:: tuple

lpos: typedef

reference_aln: bytes

reference_length: typedef

rpos: typedef

seq: bytes

unitig_aln: bytes

unitig_length: typedef

MACS3.Signal.UnitigRACollection.bool(*args, **kwargs)