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_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
def update_segmentation_in_multi_align(multiAlign, lenSegs):
multiAlignInSeg, segIds = multi_align_sep_by_seg(multiAlign, lenSegs)
return multiAlignInSeg, segIds
