From 8ef4a68a21e029f0dbdef5475b160d14ce54833a Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Thu, 14 Aug 2014 15:01:15 +0200
Subject: [PATCH] Added weights for variants.
---
mutalyzer/describe.py | 64 +++++++++++++++++++++++++++++--------------
mutalyzer/variant.py | 23 ++++++++++++++--
2 files changed, 64 insertions(+), 23 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 91d072f0..520322ba 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -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
diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py
index 5db00642..de8187d5 100644
--- a/mutalyzer/variant.py
+++ b/mutalyzer/variant.py
@@ -1,6 +1,7 @@
"""
"""
+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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