From 83ee7989201c098e8ec805380ebd810d9222874b Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 15 Aug 2014 10:04:32 +0200
Subject: [PATCH] Added weights for raw sequences.
---
mutalyzer/describe.py | 28 +++++++++++++++++++---------
1 file changed, 19 insertions(+), 9 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 7b959498..82c8d6c4 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
--
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