MACS3.Signal.RACollection module

All Parser classes

class MACS3.Signal.RACollection.RACollection

Bases: object

A collection of ReadAlignment objects and the corresponding PeakIO.

build_unitig_collection(fermiMinOverlap)

unitig_and: list tuple_alns are in the same order!

return UnitigCollection object.

get_FASTQ()

Get FASTQ file for all reads in RACollection.

get_PosReadsInfo_ref_pos(ref_pos, ref_nt, Q=20)

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

Return a PosReadsInfo object.

n_edits_sum()

remove_outliers(percent=5)

Remove outliers with too many n_edits. The outliers with n_edits in top p% will be removed.

Default: remove top 5% of reads that have too many differences with reference genome.

sort()

Sort RAs according to lpos. Should be used after realignment.