diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py index 7b9594985828efd54eeb8f19cfdcfae23ae2c5a3..82c8d6c46e963fe0f5bd8c5d72f6deb0bf67377b 100644 --- a/mutalyzer/describe.py +++ b/mutalyzer/describe.py @@ -210,13 +210,15 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar, end=var.reference_end, type="dup", shift=shift, sample_start=var.sample_start + 1, sample_end=var.sample_end, inserted=ISeqList([ISeq(sequence=s2[ - var.sample_start:var.sample_end])]), + var.sample_start:var.sample_end], + weight_position=weight_position)]), weight_position=weight_position) #if return container(start=var.reference_start, end=var.reference_start + 1, inserted=seq_list or - ISeqList([ISeq(sequence=s2[var.sample_start:var.sample_end])]), + ISeqList([ISeq(sequence=s2[var.sample_start:var.sample_end], + weight_position=weight_position)]), type="ins", shift=shift, sample_start=var.sample_start + 1, sample_end=var.sample_end, weight_position=weight_position) #if @@ -233,7 +235,8 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar, end=var.reference_end, type="del", shift=shift, sample_start=var.sample_start, sample_end=var.sample_end + 1, deleted=ISeqList([ISeq(sequence=s1[ - var.reference_start:var.reference_end])]), + var.reference_start:var.reference_end], + weight_position=weight_position)]), weight_position=weight_position) #if @@ -244,8 +247,10 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar, return container(start=var.reference_start + 1, end=var.reference_end, sample_start=var.sample_start + 1, sample_end=var.sample_end, type="subst", - deleted=ISeqList([ISeq(sequence=s1[var.reference_start])]), - inserted=ISeqList([ISeq(sequence=s2[var.sample_start])]), + deleted=ISeqList([ISeq(sequence=s1[var.reference_start], + weight_position=weight_position)]), + inserted=ISeqList([ISeq(sequence=s2[var.sample_start], + weight_position=weight_position)]), weight_position=weight_position) #if @@ -262,17 +267,22 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar, end=var.reference_end, type="inv", sample_start=var.sample_start + 1, sample_end=var.sample_end, deleted=ISeqList([ISeq(sequence=s1[ - var.reference_start:var.reference_end])]), + var.reference_start:var.reference_end], + weight_position=weight_position)]), inserted=ISeqList([ISeq(sequence=s2[ - var.sample_start:var.reference_end])]), + var.sample_start:var.reference_end], + weight_position=weight_position)]), weight_position=weight_position) #if # InDel. return container(start=var.reference_start + 1, end=var.reference_end, deleted=ISeqList([ISeq(sequence=s1[ - var.reference_start:var.reference_end])]), inserted=seq_list or - ISeqList([ISeq(sequence=s2[var.sample_start:var.sample_end])]), + var.reference_start:var.reference_end], + weight_position=weight_position)]), + inserted=seq_list or + ISeqList([ISeq(sequence=s2[var.sample_start:var.sample_end], + weight_position=weight_position)]), type="delins", sample_start=var.sample_start + 1, sample_end=var.sample_end, weight_position=weight_position) #var_to_rawvar