From 2330eadd680796542198c910c0d223969dba99e2 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 May 2022 22:33:02 +0200
Subject: [PATCH] introduce IDENTITY substitution matrix
Probably performs terrible on not super close homologues but the use case
here is to align very similar DNA/RNA sequences
---
modules/seq/alg/pymod/mat.py | 3 ++-
modules/seq/alg/pymod/wrap_seq_alg.cc | 1 +
modules/seq/alg/src/subst_weight_matrix.cc | 12 ++++++++++++
modules/seq/alg/src/subst_weight_matrix.hh | 3 ++-
4 files changed, 17 insertions(+), 2 deletions(-)
diff --git a/modules/seq/alg/pymod/mat.py b/modules/seq/alg/pymod/mat.py
index f79bf8326..57fa10c17 100644
--- a/modules/seq/alg/pymod/mat.py
+++ b/modules/seq/alg/pymod/mat.py
@@ -9,5 +9,6 @@ BLOSUM45 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM45)
BLOSUM62 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM62)
BLOSUM80 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM80)
BLOSUM100 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM100)
+IDENTITY = _InitMatrix(SubstWeightMatrix.Preset.IDENTITY)
-__all__=['BLOSUM45','BLOSUM62','BLOSUM80','BLOSUM100']
+__all__=['BLOSUM45','BLOSUM62','BLOSUM80','BLOSUM100', 'IDENTITY']
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index ebb3adb97..d0577fa5c 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -222,6 +222,7 @@ void export_contact_prediction()
.value("BLOSUM62", SubstWeightMatrix::BLOSUM62)
.value("BLOSUM80", SubstWeightMatrix::BLOSUM80)
.value("BLOSUM100", SubstWeightMatrix::BLOSUM100)
+ .value("IDENTITY", SubstWeightMatrix::IDENTITY)
;
}
diff --git a/modules/seq/alg/src/subst_weight_matrix.cc b/modules/seq/alg/src/subst_weight_matrix.cc
index f382e4f8e..454dbeddb 100644
--- a/modules/seq/alg/src/subst_weight_matrix.cc
+++ b/modules/seq/alg/src/subst_weight_matrix.cc
@@ -140,6 +140,14 @@ void FillData(ost::seq::alg::SubstWeightMatrix* subst, short (&data)[23][23]){
}
}
+void FillIdentity(ost::seq::alg::SubstWeightMatrix* subst) {
+ char chars[26] = {'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O',
+ 'P','Q','R','S','T','U','V','W','X','Y','Z'};
+ for(uint i = 0; i < 26; ++i) {
+ subst->SetWeight(chars[i], chars[i], 1.0);
+ }
+}
+
}
namespace ost { namespace seq { namespace alg {
@@ -167,6 +175,10 @@ void SubstWeightMatrix::AssignPreset(SubstWeightMatrix::Preset p)
FillData(this,RAW_BLOSUM100_DATA);
break;
}
+ case IDENTITY:{
+ FillIdentity(this);
+ break;
+ }
}
}
diff --git a/modules/seq/alg/src/subst_weight_matrix.hh b/modules/seq/alg/src/subst_weight_matrix.hh
index 25f74dc1a..fe057be1b 100644
--- a/modules/seq/alg/src/subst_weight_matrix.hh
+++ b/modules/seq/alg/src/subst_weight_matrix.hh
@@ -43,7 +43,8 @@ public:
enum Preset{BLOSUM45 = 0,
BLOSUM62 = 1,
BLOSUM80 = 2,
- BLOSUM100 = 3};
+ BLOSUM100 = 3,
+ IDENTITY = 4};
/// \brief Initialize substitution matrix with zero.
///
/// In order to get a useful substitution weight matrix, use SetWeight().
--
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