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Commit 4559a557 authored by Vermaat's avatar Vermaat
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Fixup for bc0377a6 where we forgot many RawVar renames

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with 38 additions and 34 deletions
mutalyzer/describe.py
+ 38
− 34
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......@@ -281,6 +281,10 @@ class DescribeRawVar(models.RawVar):
Example: if {end} is initialised for a substitution, a range will be
retuned, resulting in a description like: 100_100A>T
Note: As a workaround for a classname conflict in Spyne, this class is
named `DescribeRawVar` instead of just `RawVar`. We might want to reconsider
this name at some point.
"""
def __init__(self, DNA=True, start=0, start_offset=0, end=0, end_offset=0,
......@@ -477,14 +481,14 @@ class DescribeRawVar(models.RawVar):
return self.__DNADescriptionLength()
return self.__proteinDescriptionLength()
#descriptionLength
#RawVar
#DescribeRawVar
def alleleDescription(allele):
"""
Convert a list of raw variants to an HGVS allele description.
@arg allele: A list of raw variants representing an allele description.
@type allele: list(RawVar)
@type allele: list(DescribeRawVar)
@returns: The HGVS description of {allele}.
@rval: str
......@@ -499,7 +503,7 @@ def alleleDescriptionLength(allele):
Calculate the standardised length of an HGVS allele description.
@arg allele: A list of raw variants representing an allele description.
@type allele: list(RawVar)
@type allele: list(DescribeRawVar)
@returns: The standardised length of the HGVS description of {allele}.
@rval: int
......@@ -538,8 +542,8 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
arg s2_end: End of the range on {s2}.
type s2_end: int
@returns: A list of RawVar objects, representing the allele.
@rval: list(RawVar)
@returns: A list of DescribeRawVar objects, representing the allele.
@rval: list(DescribeRawVar)
"""
# TODO: Instead of copying this function and adjusting it to make it work
# for proteins, consider disabling parts like the inversion.
......@@ -547,7 +551,7 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
# Nothing happened.
if s1 == s2:
return [RawVar()]
return [DescribeRawVar()]
# Insertion / Duplication.
if s1_start == s1_end:
......@@ -564,11 +568,11 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
s1[s1_start - ins_length:s1_start] == s2[s2_start:s2_end]:
if ins_length == 1:
return [RawVar(start=s1_start, type="dup", shift=shift)]
return [RawVar(start=s1_start - ins_length + 1, end=s1_end,
return [DescribeRawVar(start=s1_start, type="dup", shift=shift)]
return [DescribeRawVar(start=s1_start - ins_length + 1, end=s1_end,
type="dup", shift=shift)]
#if
return [RawVar(start=s1_start, end=s1_start + 1,
return [DescribeRawVar(start=s1_start, end=s1_start + 1,
inserted=s2[s2_start:s2_end], type="ins", shift=shift)]
#if
......@@ -581,18 +585,18 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
s1_end += shift3
if s1_start == s1_end:
return [RawVar(start=s1_start, type="del", shift=shift)]
return [RawVar(start=s1_start, end=s1_end, type="del", shift=shift)]
return [DescribeRawVar(start=s1_start, type="del", shift=shift)]
return [DescribeRawVar(start=s1_start, end=s1_end, type="del", shift=shift)]
#if
# Substitution.
if s1_start + 1 == s1_end and s2_start + 1 == s2_end:
return [RawVar(start=s1_start + 1, deleted=s1[s1_start],
return [DescribeRawVar(start=s1_start + 1, deleted=s1[s1_start],
inserted=s2[s2_start], type="subst")]
# Simple InDel.
if s1_start + 1 == s1_end:
return [RawVar(start=s1_start + 1, inserted=s2[s2_start:s2_end],
return [DescribeRawVar(start=s1_start + 1, inserted=s2[s2_start:s2_end],
type="delins")]
# TODO: Refactor the code after this point.
......@@ -610,7 +614,7 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
lcs_r_len = 0 # s1_end_r and s2_end_r should not be used after this.
# Inversion or Compound variant.
default = [RawVar(start=s1_start + 1, end=s1_end,
default = [DescribeRawVar(start=s1_start + 1, end=s1_end,
inserted=s2[s2_start:s2_end], type="delins")]
if not (lcs_f_len or lcs_r_len) : # Optimisation, not really needed.
......@@ -626,7 +630,7 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
# Simple Inversion.
if s2_end - s2_start == lcs_r_len and s1_end - s1_start == lcs_r_len:
return [RawVar(start=s1_start + 1, end=s1_end, type="inv")]
return [DescribeRawVar(start=s1_start + 1, end=s1_end, type="inv")]
r1_len = s1_end_r - lcs_r_len
r2_len = s1_end - s1_start - s1_end_r
......@@ -651,7 +655,7 @@ def DNA_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
s1_end - r2_len + lcp, s1_end, s2_end - m1_len + lcp, s2_end)
#if
partial = leftRv + [RawVar(start=s1_start + r1_len + 1,
partial = leftRv + [DescribeRawVar(start=s1_start + r1_len + 1,
end=s1_end - r2_len, type="inv")] + rightRv
#if
......@@ -690,29 +694,29 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
arg s2_end: End of the range on {s2}.
type s2_end: int
@returns: A list of RawVar objects, representing the allele.
@rval: list(RawVar)
@returns: A list of DescribeRawVar objects, representing the allele.
@rval: list(DescribeRawVar)
"""
if s1 == '?' or s2 == '?':
return [RawVar(DNA=False, type="unknown")]
return [DescribeRawVar(DNA=False, type="unknown")]
# One of the sequences is missing.
if not (s1 and s2):
return [RawVar(DNA=False)]
return [DescribeRawVar(DNA=False)]
# Nothing happened.
if s1 == s2:
return [RawVar(DNA=False)]
return [DescribeRawVar(DNA=False)]
# Substitution.
if s1_start + 1 == s1_end and s2_start + 1 == s2_end:
return [RawVar(DNA=False, start=s1_start + 1, deleted=s1[s1_start],
return [DescribeRawVar(DNA=False, start=s1_start + 1, deleted=s1[s1_start],
inserted=s2[s2_start], type="subst")]
# Insertion / Duplication / Extention.
if s1_start == s1_end:
if len(s1) == s1_start + 1:
return [RawVar(DNA=False, start=s1_start + 1,
return [DescribeRawVar(DNA=False, start=s1_start + 1,
inserted=s2[s2_start], term=abs(len(s1) - len(s2)),
type="ext")]
ins_length = s2_end - s2_start
......@@ -728,13 +732,13 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
s1[s1_start - ins_length:s1_start] == s2[s2_start:s2_end]:
if ins_length == 1:
return [RawVar(DNA=False, start=s1_start,
return [DescribeRawVar(DNA=False, start=s1_start,
startAA=s1[s1_start - 1], type="dup", shift=shift)]
return [RawVar(DNA=False, start=s1_start - ins_length + 1,
return [DescribeRawVar(DNA=False, start=s1_start - ins_length + 1,
startAA=s1[s1_start - ins_length], end=s1_end,
endAA=s1[s1_end - 1], type="dup", shift=shift)]
#if
return [RawVar(DNA=False, start=s1_start, startAA=s1[s1_start - 1],
return [DescribeRawVar(DNA=False, start=s1_start, startAA=s1[s1_start - 1],
end=s1_start + 1, endAA=s1[s1_end], inserted=s2[s2_start:s2_end],
type="ins", shift=shift)]
#if
......@@ -742,7 +746,7 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
# Deletion / Inframe stop.
if s2_start == s2_end:
if len(s2) == s2_end + 1:
return [RawVar(DNA=False, start=s1_start + 1, startAA=s1[s1_start],
return [DescribeRawVar(DNA=False, start=s1_start + 1, startAA=s1[s1_start],
type="stop")]
shift5, shift3 = roll(s1, s1_start + 1, s1_end)
shift = shift5 + shift3
......@@ -751,15 +755,15 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
s1_end += shift3
if s1_start == s1_end:
return [RawVar(DNA=False, start=s1_start, startAA=s1[s1_start - 1],
return [DescribeRawVar(DNA=False, start=s1_start, startAA=s1[s1_start - 1],
type="del", shift=shift)]
return [RawVar(DNA=False, start=s1_start, startAA=s1[s1_start - 1],
return [DescribeRawVar(DNA=False, start=s1_start, startAA=s1[s1_start - 1],
end=s1_end, endAA=s1[s1_end - 1], type="del", shift=shift)]
#if
# Simple InDel.
if s1_start + 1 == s1_end:
return [RawVar(DNA=False, start=s1_start + 1, startAA=s1[s1_start],
return [DescribeRawVar(DNA=False, start=s1_start + 1, startAA=s1[s1_start],
inserted=s2[s2_start:s2_end], type="delins")]
# Frameshift.
......@@ -771,7 +775,7 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
fitFS(s1[s1_start + 1:], s2[s2_start + 1:], FS2) or
fitFS(s2[s2_start + 1:], s1[s1_start + 2:], FS1) or
fitFS(s2[s2_start + 1:], s1[s1_start + 2:], FS2)):
return [RawVar(DNA=False, start=s1_start + 1, deleted=s1[s1_start],
return [DescribeRawVar(DNA=False, start=s1_start + 1, deleted=s1[s1_start],
inserted=s2[s2_start], term=len(s2) - s2_start, type="fs")]
#if
......@@ -780,7 +784,7 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
(s2_start, s2_end))
# InDel.
default = [RawVar(DNA=False, start=s1_start + 1, startAA=s1[s1_start],
default = [DescribeRawVar(DNA=False, start=s1_start + 1, startAA=s1[s1_start],
end=s1_end, endAA=s1[s1_end], inserted=s2[s2_start:s2_end],
type="delins")]
......@@ -810,8 +814,8 @@ def describe(original, mutated, DNA=True):
@arg mutated:
@type mutated: str
@returns: A list of RawVar objects, representing the allele.
@rval: list(RawVar)
@returns: A list of DescribeRawVar objects, representing the allele.
@rval: list(DescribeRawVar)
"""
s1 = str(original)
s2 = str(mutated)
......
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