def update_segmentation_in_multi_aling_all_seg(multiAlign, lenSegs): """ update multiple alignments in segments under new segmentation note that because the number of segments changes, the segRateDict also changes, which also need to be updated input: lenSegs: length of segments rateSegs: estimated rate index in each segment ratesList: list, all rates multiAlign: multiple alignment, seqName -> string output: multiAlignAllSeg: dict, pair->segId->pairwise alignment (non empty pairs only, i.e., no ['-', '-']) """ multiAlignInSeg, segIds = multi_align_sep_by_seg(multiAlign, lenSegs) multiAlignAllSeg = get_multi_align_in_all_seg(multiAlignInSeg, segIds) return multiAlignAllSeg
def update_segmentation_in_multi_align(multiAlign, lenSegs): multiAlignInSeg, segIds = multi_align_sep_by_seg(multiAlign, lenSegs) return multiAlignInSeg, segIds