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Commit 8ef4a68a authored by Laros's avatar Laros Committed by Vermaat
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Added weights for variants.

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mutalyzer/describe.py
+ 44
− 20
View file @ 8ef4a68a
......@@ -181,16 +181,28 @@ def find_fs(peptide, alternative_peptide, fs):
#find_fs
def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
def var_to_rawvar(s1, s2, var, weight_position, seq_list=[], container=DNAVar):
"""
"""
# Unknown.
if s1 == '?' or s2 == '?':
return [container(type="unknown")]
ins_length = var.sample_end - var.sample_start
weight = 0
if seq_list:
inserted = seq_list
weight = seq_list.weight()
else:
inserted = ISeqList([ISeq(
sequence=s2[var.sample_start:var.sample_end],
weight=ins_length)])
# Insertion / Duplication.
if var.reference_start == var.reference_end:
ins_length = var.sample_end - var.sample_start
shift5, shift3 = roll(s2, var.sample_start + 1, var.sample_end)
shift = shift5 + shift3
......@@ -199,6 +211,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
var.sample_start += shift3
var.sample_end += shift3
# FIXME: range can be a duplication.
if not seq_list and (var.sample_start - ins_length >= 0 and
s1[var.reference_start - ins_length:var.reference_start] ==
s2[var.sample_start:var.sample_end]):
......@@ -207,14 +220,16 @@ 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=var.weight)
#if
weight += (2 * weight_position + extractor.WEIGHT_SEPARATOR +
extractor.WEIGHT_INSERTION)
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])]),
type="ins", shift=shift, sample_start=var.sample_start + 1,
sample_end=var.sample_end)
end=var.reference_start + 1, inserted=inserted, type="ins",
shift=shift, sample_start=var.sample_start + 1,
sample_end=var.sample_end, weight=weight)
#if
# Deletion.
......@@ -228,7 +243,7 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
return container(start=var.reference_start + 1,
end=var.reference_end, type="del", shift=shift,
sample_start=var.sample_start, sample_end=var.sample_end + 1,
deleted=ISeqList([ISeq(sequence=s1[
weight=var.weight, deleted=ISeqList([ISeq(sequence=s1[
var.reference_start:var.reference_end])]))
#if
......@@ -238,7 +253,7 @@ 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",
sample_end=var.sample_end, type="subst", weight=var.weight,
deleted=ISeqList([ISeq(sequence=s1[var.reference_start])]),
inserted=ISeqList([ISeq(sequence=s2[var.sample_start])]))
#if
......@@ -258,16 +273,19 @@ def var_to_rawvar(s1, s2, var, seq_list=[], container=DNAVar):
deleted=ISeqList([ISeq(sequence=s1[
var.reference_start:var.reference_end])]),
inserted=ISeqList([ISeq(sequence=s2[
var.sample_start:var.reference_end])]))
var.sample_start:var.reference_end])]), weight=var.weight)
#if
# InDel.
weight += weight_position + extractor.WEIGHT_DELETION_INSERTION
if var.reference_start + 1 == var.reference_end:
weight += weight_position + extractor.WEIGHT_SEPARATOR
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])]), inserted=seq_list,
type="delins", sample_start=var.sample_start + 1,
sample_end=var.sample_end)
sample_end=var.sample_end, weight=var.weight)
#var_to_rawvar
def describe_dna(s1, s2):
......@@ -285,7 +303,8 @@ def describe_dna(s1, s2):
description = Allele()
in_transposition = 0
for variant in extractor.extract(str(s1), len(s1), str(s2), len(s2), 0):
variant_extract = extractor.extract(str(s1), len(s1), str(s2), len(s2), 0)
for variant in variant_extract.variants:
print (variant.type, variant.reference_start,
variant.reference_end, variant.sample_start,
variant.sample_end, variant.transposition_start,
......@@ -302,22 +321,27 @@ def describe_dna(s1, s2):
if in_transposition:
if variant.type & extractor.IDENTITY:
seq_list.append(ISeq(start=variant.transposition_start + 1,
end=variant.transposition_end, reverse=False))
end=variant.transposition_end, weight=variant.weight,
reverse=False))
elif variant.type & extractor.REVERSE_COMPLEMENT:
seq_list.append(ISeq(start=variant.transposition_start + 1,
end=variant.transposition_end, reverse=True))
end=variant.transposition_end, weight=variant.weight,
reverse=True))
else:
seq_list.append(ISeq(
sequence=s2[variant.sample_start:variant.sample_end]))
sequence=s2[variant.sample_start:variant.sample_end],
weight=variant.weight))
#if
elif not (variant.type & extractor.IDENTITY):
description.append(var_to_rawvar(s1, s2, variant))
description.append(var_to_rawvar(s1, s2, variant,
variant_extract.weight_position))
if variant.type & extractor.TRANSPOSITION_CLOSE:
in_transposition -= 1
if not in_transposition:
description.append(var_to_rawvar(s1, s2, variant, seq_list))
description.append(var_to_rawvar(s1, s2, variant,
variant_extract.weight_position, seq_list))
#if
#for
......
mutalyzer/variant.py
+ 20
− 3
View file @ 8ef4a68a
"""
"""
from extractor.extractor import WEIGHT_SEPARATOR
from mutalyzer import models
class HGVSList(list):
......@@ -12,6 +13,13 @@ class HGVSList(list):
return "[{}]".format(';'.join(map(str, self)))
return str(self[0])
#__str__
def weight(self):
W = sum(map(lambda x: x.weight, self))
if len(self) > 1:
return W + (len(self) + 1) * WEIGHT_SEPARATOR
return W
#HGVSList
class Allele(HGVSList):
......@@ -24,7 +32,7 @@ class ISeq(object):
"""
Container for an inserted sequence.
"""
def __init__(self, sequence="", start=0, end=0, reverse=False):
def __init__(self, sequence="", start=0, end=0, weight=0, reverse=False):
"""
:arg sequence: Literal inserted sequence.
:type sequence: str
......@@ -32,12 +40,15 @@ class ISeq(object):
:type start: int
:arg end: End position for a transposed sequence.
:type end: int
:arg weight: Weight of the variant (normalised length).
:type weight: int
:arg reverse: Inverted transposed sequence.
:type reverse: bool
"""
self.sequence = sequence
self.start = start
self.end = end
self.weight = weight
self.reverse = reverse
self.type = "trans"
......@@ -64,7 +75,7 @@ class DNAVar(models.DNAVar):
def __init__(self, start=0, start_offset=0, end=0, end_offset=0,
sample_start=0, sample_start_offset=0, sample_end=0,
sample_end_offset=0, type="none", deleted=ISeqList([ISeq()]),
inserted=ISeqList([ISeq()]), shift=0):
inserted=ISeqList([ISeq()]), weight=0, shift=0):
"""
Initialise the class with the appropriate values.
......@@ -90,6 +101,8 @@ class DNAVar(models.DNAVar):
:type deleted: str
:arg inserted: Inserted part.
:type inserted: object
:arg weight: Weight of the variant (normalised length).
:type weight: int
:arg shift: Amount of freedom.
:type shift: int
"""
......@@ -106,6 +119,7 @@ class DNAVar(models.DNAVar):
self.type = type
self.deleted = deleted
self.inserted = inserted
self.weight = weight
self.shift = shift
#__init__
......@@ -144,7 +158,7 @@ class ProteinVar(models.ProteinVar):
"""
def __init__(self, start=0, end=0, sample_start=0, sample_end=0,
type="none", deleted=ISeqList([ISeq()]),
inserted=ISeqList([ISeq()]), shift=0, term=0):
inserted=ISeqList([ISeq()]), weight=0, shift=0, term=0):
"""
Initialise the class with the appropriate values.
......@@ -162,6 +176,8 @@ class ProteinVar(models.ProteinVar):
:type deleted: str
:arg inserted: Inserted part.
:type inserted: object
:arg weight: Weight of the variant (normalised length).
:type weight: int
:arg shift: Amount of freedom.
:type shift: int
:arg term:
......@@ -174,6 +190,7 @@ class ProteinVar(models.ProteinVar):
self.type = type
self.deleted = deleted
self.inserted = inserted
self.weight = weight
self.shift = shift
self.term = term
#__init__
......
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