From 0546f80f865c9ba62e59b280e8e30c4b5189a19a Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 26 May 2011 14:31:33 +0200
Subject: [PATCH] Added function seq.alg.GlobalAlign
---
modules/seq/alg/doc/seqalg.rst | 36 +++++-
modules/seq/alg/pymod/wrap_seq_alg.cc | 5 +-
modules/seq/alg/src/CMakeLists.txt | 2 +
modules/seq/alg/src/global_align.cc | 97 ++++++++++++++
modules/seq/alg/src/global_align.hh | 35 +++++
modules/seq/alg/src/impl/align_impl.hh | 143 +++++++++++++++++++++
modules/seq/alg/src/local_align.cc | 107 ++-------------
modules/seq/alg/tests/CMakeLists.txt | 1 +
modules/seq/alg/tests/test_global_align.py | 50 +++++++
9 files changed, 378 insertions(+), 98 deletions(-)
create mode 100644 modules/seq/alg/src/global_align.cc
create mode 100644 modules/seq/alg/src/global_align.hh
create mode 100644 modules/seq/alg/src/impl/align_impl.hh
create mode 100644 modules/seq/alg/tests/test_global_align.py
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index 4475202dd..cf3587d06 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -39,8 +39,8 @@
.. function:: LocalAlign(seq1, seq2, subst_weight, gap_open=-5, gap_ext=-2)
- Performs a Smith/Waterman local alignment of *seq1* and *seq2* and returns the
- best-scoring alignments as a list of pairwise alignments.
+ Performs a Smith/Waterman local alignment of *seq1* and *seq2* and returns
+ the best-scoring alignments as a list of pairwise alignments.
**Example:**
@@ -63,5 +63,33 @@
:param gap_open: The gap opening penalty. Must be a negative number
:param gap_ext: The gap extension penalty. Must be a negative number
:returns: list of best-scoring, non-overlapping alignments of *seq1* and
- *seq2*. The start of the alignments is stored in the sequence offset of the
- two sequences.
\ No newline at end of file
+ *seq2*. Since alignments always start with a replacement, the start is
+ stored in the sequence offset of the two sequences.
+
+
+.. function:: GlobalAlign(seq1, seq2, subst_weight, gap_open=-5, gap_ext=-2)
+
+ Performs a Needleman/Wunsch global alignment of *seq1* and *seq2* and returns
+ the best-scoring alignment.
+
+ **Example:**
+
+ .. code-block:: python
+
+ seq_a=seq.CreateSequence('A', 'acdefghiklmn')
+ seq_b=seq.CreateSequence('B', 'acdhiklmn')
+ alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
+ print alns[0].ToString(80)
+ # >>> A acdefghiklmn
+ # >>> B acd---hiklmn
+
+ :param seq1: A valid sequence
+ :type seq1: :class:`~ost.seq.ConstSequenceHandle`
+ :param seq2: A valid sequence
+ :type seq2: :class:`~ost.seq.ConstSequenceHandle`
+
+ :param subst_weigth: The substitution weights matrix
+ :type subst_weight: :class:`SubstWeightMatrix`
+ :param gap_open: The gap opening penalty. Must be a negative number
+ :param gap_ext: The gap extension penalty. Must be a negative number
+ :returns: best-scoring alignment of *seq1* and *seq2*.
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 6257b736f..f8324daa8 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -25,6 +25,7 @@
#include <ost/seq/alg/conservation.hh>
#include <ost/seq/alg/subst_weight_matrix.hh>
#include <ost/seq/alg/local_align.hh>
+#include <ost/seq/alg/global_align.hh>
using namespace boost::python;
using namespace ost::seq;
using namespace ost::seq::alg;
@@ -53,7 +54,9 @@ BOOST_PYTHON_MODULE(_seq_alg)
;
def("MergePairwiseAlignments", &MergePairwiseAlignments);
def("Conservation", &Conservation, (arg("assign")=true, arg("prop_name")="cons"));
- def("LocalAlign", &LocalAlign, (arg("seq1"), arg("seq2"), arg("subst_weight"),
+ def("LocalAlign", &LocalAlign, (arg("seq1"), arg("seq2"),arg("subst_weight"),
+ arg("gap_open")=-5, arg("gap_ext")=-2));
+ def("GlobalAlign", &GlobalAlign,(arg("seq1"),arg("seq2"),arg("subst_weight"),
arg("gap_open")=-5, arg("gap_ext")=-2));
}
diff --git a/modules/seq/alg/src/CMakeLists.txt b/modules/seq/alg/src/CMakeLists.txt
index b45f036cb..507869bcb 100644
--- a/modules/seq/alg/src/CMakeLists.txt
+++ b/modules/seq/alg/src/CMakeLists.txt
@@ -7,11 +7,13 @@ alignment_opts.hh
merge_pairwise_alignments.hh
conservation.hh
local_align.hh
+global_align.hh
)
set(OST_SEQ_ALG_SOURCES
merge_pairwise_alignments.cc
local_align.cc
+global_align.cc
sequence_identity.cc
ins_del.cc
subst_weight_matrix.cc
diff --git a/modules/seq/alg/src/global_align.cc b/modules/seq/alg/src/global_align.cc
new file mode 100644
index 000000000..ad8275c9c
--- /dev/null
+++ b/modules/seq/alg/src/global_align.cc
@@ -0,0 +1,97 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <ost/log.hh>
+#include "impl/align_impl.hh"
+#include "global_align.hh"
+
+namespace ost { namespace seq { namespace alg {
+
+void Traceback(impl::AlnMat& mat, int max_i, int max_j,
+ const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ AlignmentList& alignments)
+{
+ int i = (max_i > 0 ? max_i-1 : 0);
+ int j = (max_j > 0 ? max_j-1 : 0);
+ String aln_str1;
+ String aln_str2;
+ while (i > 0 || j > 0) {
+ impl::SetRoute(mat, i, j, s1, s2, aln_str1, aln_str2);
+ }
+ impl::StoreStrAsAln(aln_str1, aln_str2, s1, s2, i, j, alignments);
+}
+
+AlignmentList GlobalAlign(const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ alg::SubstWeightMatrixPtr& subst,
+ int gap_open,int gap_ext)
+{
+ impl::AlnMat mat(s1.GetLength()+1, s2.GetLength()+1);
+ // init first column of matrix
+ if (mat.GetHeight() > 1) {
+ mat(0, 1).score = mat(0, 0).score + gap_open;
+ mat(0, 1).from = impl::INS1;
+ }
+ for (int j = 2; j < mat.GetHeight(); ++j) {
+ mat(0, j).score = mat(0, j-1).score + gap_ext;
+ mat(0, j).from = impl::INS1;
+ }
+ // fill the alignment matrix
+ for (int i = 0; i < mat.GetWidth()-1; ++i) {
+ mat(i+1, 0).score = mat(i, 0).score
+ + (mat(i, 0).from==impl::INS2 ? gap_ext : gap_open);
+ mat(i+1,0).from = impl::INS2;
+ for (int j = 0; j < mat.GetHeight()-1; ++j) {
+ char c1=s1[i];
+ char c2=s2[j];
+ short weight=subst->GetWeight(c1, c2);
+ int diag=weight+mat(i, j).score;
+ int ins1=mat(i+1, j).score
+ +(mat(i+1, j).from==impl::INS1 ? gap_ext : gap_open);
+ int ins2=mat(i, j+1).score
+ +(mat(i, j+1).from==impl::INS2 ? gap_ext : gap_open);
+ if (diag>=ins1) {
+ if (diag>=ins2) {
+ mat(i+1, j+1).score=diag;
+ mat(i+1, j+1).from=impl::DIAG;
+ } else {
+ mat(i+1, j+1).score=ins2;
+ mat(i+1, j+1).from=impl::INS2;
+ }
+ } else if (ins1>ins2) {
+ mat(i+1, j+1).score=ins1;
+ mat(i+1, j+1).from=impl::INS1;
+ } else {
+ mat(i+1, j+1).score=ins2;
+ mat(i+1, j+1).from=impl::INS2;
+ }
+ }
+ }
+ // write traceback matrix in debug mode
+#if !defined(NDEBUG)
+ DbgWriteAlnMatrix(mat,s1, s2);
+#endif
+ AlignmentList alignments;
+ Traceback(mat, mat.GetWidth(), mat.GetHeight(), s1, s2, alignments);
+ LOG_DEBUG(alignments.back().ToString(80));
+
+ return alignments;
+}
+
+}}}
diff --git a/modules/seq/alg/src/global_align.hh b/modules/seq/alg/src/global_align.hh
new file mode 100644
index 000000000..a920832d7
--- /dev/null
+++ b/modules/seq/alg/src/global_align.hh
@@ -0,0 +1,35 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_ALG_GLOBAL_ALIGN_HH
+#define OST_SEQ_ALG_GLOBAL_ALIGN_HH
+
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/subst_weight_matrix.hh>
+#include "module_config.hh"
+
+namespace ost { namespace seq { namespace alg {
+
+
+AlignmentList DLLEXPORT_OST_SEQ_ALG GlobalAlign(const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ SubstWeightMatrixPtr& subst,
+ int gap_open=-5,int gap_ext=-2);
+}}}
+
+#endif
diff --git a/modules/seq/alg/src/impl/align_impl.hh b/modules/seq/alg/src/impl/align_impl.hh
new file mode 100644
index 000000000..866b569ae
--- /dev/null
+++ b/modules/seq/alg/src/impl/align_impl.hh
@@ -0,0 +1,143 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_ALIGN_IMPL_HH
+#define OST_ALIGN_IMPL_HH
+
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/subst_weight_matrix.hh>
+//#include "module_config.hh"
+
+namespace ost { namespace seq { namespace alg { namespace impl {
+
+ typedef enum {
+ DIAG,
+ INS1,
+ INS2,
+ UNKN
+ } Path;
+
+ struct DLLEXPORT AlnPos {
+ AlnPos(): score(0), from(impl::UNKN) { }
+ int score;
+ impl::Path from;
+ };
+
+ struct DLLEXPORT AlnMat {
+ AlnMat(int width, int height):
+ mat_(width*height), width_(width), height_(height)
+ { }
+
+ impl::AlnPos& operator()(int x, int y) { return mat_[x*height_+y]; }
+
+ const impl::AlnPos& operator()(int x, int y) const {
+ return mat_[x*height_+y];
+ }
+
+ int GetWidth() const { return width_; }
+ int GetHeight() const { return height_; }
+
+ private:
+ std::vector<impl::AlnPos> mat_;
+ int width_;
+ int height_;
+};
+
+inline void DLLEXPORT SetRoute(impl::AlnMat& mat, int& i, int& j,
+ const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ String& aln_str1, String& aln_str2)
+{
+ switch (mat(i, j).from) {
+ case impl::DIAG:
+ --i;
+ --j;
+ aln_str1.push_back(s1[i]);
+ aln_str2.push_back(s2[j]);
+ break;
+ case impl::INS1:
+ --j;
+ aln_str1.push_back('-');
+ aln_str2.push_back(s2[j]);
+ break;
+ case impl::INS2:
+ --i;
+ aln_str1.push_back(s1[i]);
+ aln_str2.push_back('-');
+ break;
+ default:
+ assert(0 && "should never get here");
+ }
+};
+
+inline void DLLEXPORT StoreStrAsAln(String& aln_str1, String& aln_str2,
+ const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ const int i, const int j,
+ AlignmentList& alignments)
+{
+ for (size_t x=0; x<aln_str1.size()/2; ++x) {
+ std::swap(aln_str1[x], aln_str1[aln_str1.size()-x-1]);
+ std::swap(aln_str2[x], aln_str2[aln_str1.size()-x-1]);
+ }
+ AlignmentHandle aln=CreateAlignment();
+ aln.AddSequence(CreateSequence(s1.GetName(), aln_str1));
+ aln.AddSequence(CreateSequence(s2.GetName(), aln_str2));
+ aln.SetSequenceOffset(0, i);
+ aln.SetSequenceOffset(1, j);
+ alignments.push_back(aln);
+};
+
+#if !defined(NDEBUG)
+inline void DLLEXPORT DbgWriteAlnMatrix(impl::AlnMat& mat,
+ const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2)
+{
+ std::stringstream ss;
+ ss << " ";
+ for (int j = 1; j < mat.GetHeight(); ++j) {
+ ss << s2[j-1];
+ }
+ ss << std::endl;
+ for (int i = 0; i < mat.GetWidth(); ++i) {
+ for (int j = 0; j < mat.GetHeight(); ++j) {
+ if (j==0 && i>0) {
+ ss << s1[i-1] << " ";
+ }
+ if (i==0 && j==0) {
+ ss << " ";
+ }
+ if (mat(i, j).from==impl::DIAG) {
+ ss << "\\";
+ } else if (mat(i, j).from==impl::INS1) {
+ ss << "-";
+ } else if (mat(i, j).from==impl::INS2) {
+ ss << "|";
+ } else if (mat(i, j).from==impl::UNKN) {
+ ss << "$";
+ }
+ }
+ ss << std::endl;
+ }
+ LOG_DEBUG(ss.str());
+};
+#endif
+
+}}}}
+
+#endif
diff --git a/modules/seq/alg/src/local_align.cc b/modules/seq/alg/src/local_align.cc
index 963c81eb6..aec7a5932 100644
--- a/modules/seq/alg/src/local_align.cc
+++ b/modules/seq/alg/src/local_align.cc
@@ -17,42 +17,12 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <ost/log.hh>
+#include "impl/align_impl.hh"
#include "local_align.hh"
namespace ost { namespace seq { namespace alg {
-typedef enum {
- DIAG,
- INS1,
- INS2,
- UNKN
-} Path;
-
-struct AlnPos {
- AlnPos(): score(0), from(UNKN) { }
- int score;
- Path from;
-};
-
-struct AlnMat {
- AlnMat(int width, int height):
- mat_(width*height), width_(width), height_(height)
- { }
-
- AlnPos& operator()(int x, int y) { return mat_[x*height_+y]; }
-
- const AlnPos& operator()(int x, int y) const { return mat_[x*height_+y]; }
-
- int GetWidth() const { return width_; }
- int GetHeight() const { return height_; }
-
-private:
- std::vector<AlnPos> mat_;
- int width_;
- int height_;
-};
-
-bool CollectPatches(AlnMat& mat, int min_i, int max_i, int min_j, int max_j,
+bool CollectPatches(impl::AlnMat& mat, int min_i, int max_i, int min_j, int max_j,
const ConstSequenceHandle& s1,
const ConstSequenceHandle& s2,
AlignmentList& alignments)
@@ -71,41 +41,12 @@ bool CollectPatches(AlnMat& mat, int min_i, int max_i, int min_j, int max_j,
String aln_str1;
String aln_str2;
while (i>min_i && j>min_j && mat(i, j).score>0) {
- switch (mat(i, j).from) {
- case DIAG:
- --i;
- --j;
- aln_str1.push_back(s1[i]);
- aln_str2.push_back(s2[j]);
- break;
- case INS1:
- --j;
- aln_str1.push_back('-');
- aln_str2.push_back(s2[j]);
- break;
- case INS2:
- --i;
- aln_str1.push_back(s1[i]);
- aln_str2.push_back('-');
- break;
- default:
- assert(0 && "should never get here");
- }
+ impl::SetRoute(mat, i, j, s1, s2, aln_str1, aln_str2);
}
if (aln_str1.size()<2) {
return false;
}
- for (size_t x=0; x<aln_str1.size()/2; ++x) {
- std::swap(aln_str1[x], aln_str1[aln_str1.size()-x-1]);
- std::swap(aln_str2[x], aln_str2[aln_str1.size()-x-1]);
- }
- AlignmentHandle aln=CreateAlignment();
- aln.AddSequence(CreateSequence(s1.GetName(), aln_str1));
- aln.AddSequence(CreateSequence(s2.GetName(), aln_str2));
- aln.SetSequenceOffset(0, i);
- aln.SetSequenceOffset(1, j);
- alignments.push_back(aln);
- // clear used regions
+ impl::StoreStrAsAln(aln_str1, aln_str2, s1, s2, i, j, alignments);
for (int x=i; x<=mmax_i; ++x) {
for (int y=0; y<mat.GetHeight(); ++y) {
mat(x, y).score=0;
@@ -124,58 +65,38 @@ AlignmentList LocalAlign(const ConstSequenceHandle& s1,
alg::SubstWeightMatrixPtr& subst,
int gap_open, int gap_ext)
{
- AlnMat mat(s1.GetLength()+1, s2.GetLength()+1);
+ impl::AlnMat mat(s1.GetLength()+1, s2.GetLength()+1);
for (int i=0; i<mat.GetWidth()-1; ++i) {
for (int j=0; j<mat.GetHeight()-1; ++j) {
char c1=s1[i];
char c2=s2[j];
short weight=subst->GetWeight(c1, c2);
int diag=weight+mat(i, j).score;
- int ins1=mat(i+1, j).score+(mat(i+1, j).from==INS1 ? gap_ext : gap_open);
+ int ins1=mat(i+1, j).score
+ +(mat(i+1, j).from==impl::INS1 ? gap_ext : gap_open);
ins1=std::max(0, ins1);
- int ins2=mat(i, j+1).score+(mat(i, j+1).from==INS2 ? gap_ext : gap_open);
+ int ins2=mat(i, j+1).score
+ +(mat(i, j+1).from==impl::INS2 ? gap_ext : gap_open);
ins2=std::max(0, ins2);
if (diag>=ins1) {
if (diag>=ins2) {
mat(i+1, j+1).score=diag;
- mat(i+1, j+1).from=DIAG;
+ mat(i+1, j+1).from=impl::DIAG;
} else {
mat(i+1, j+1).score=ins2;
- mat(i+1, j+1).from=INS2;
+ mat(i+1, j+1).from=impl::INS2;
}
} else if (ins1>ins2) {
mat(i+1, j+1).score=ins1;
- mat(i+1, j+1).from=INS1;
+ mat(i+1, j+1).from=impl::INS1;
} else {
mat(i+1, j+1).score=ins2;
- mat(i+1, j+1).from=INS2;
+ mat(i+1, j+1).from=impl::INS2;
}
}
}
#if !defined(NDEBUG)
- std::stringstream ss;
- for (int i=0; i<mat.GetWidth(); ++i) {
- for (int j=0; j<mat.GetHeight(); ++j) {
- if (mat(i, j).from==DIAG) {
- ss << "\\";
- } else if (mat(i, j).from==INS1) {
- ss << "-";
- } else if (mat(i, j).from==INS2) {
- ss << "|";
- }
- if (i==0 && j>0) {
- ss << s2[j-1];
- }
- if (j==0 && i>0) {
- ss << s1[i-1] << " ";
- }
- if (i==0 && j==0) {
- ss << " ";
- }
- }
- ss << std::endl;
- }
- LOG_DEBUG(ss.str());
+ DbgWriteAlnMatrix(mat,s1, s2);
#endif
AlignmentList alignments;
while (CollectPatches(mat, 0, mat.GetWidth(), 0, mat.GetHeight(),
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 53053090e..f6d8ebe14 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -4,6 +4,7 @@ set(OST_SEQ_ALG_UNIT_TESTS
tests.cc
test_renumber.py
test_local_align.py
+ test_global_align.py
)
ost_unittest(seq_alg "${OST_SEQ_ALG_UNIT_TESTS}")
diff --git a/modules/seq/alg/tests/test_global_align.py b/modules/seq/alg/tests/test_global_align.py
new file mode 100644
index 000000000..aed51741b
--- /dev/null
+++ b/modules/seq/alg/tests/test_global_align.py
@@ -0,0 +1,50 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import seq
+from ost.bindings.clustalw import *
+
+class TestGlobalAlign(unittest.TestCase):
+ def testDeletionInSeqB(self):
+ seq_a=seq.CreateSequence('A', 'aacdefghiklmn')
+ seq_b=seq.CreateSequence('B', 'acdhiklmn')
+ alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
+ self.assertEqual(len(alns), 1)
+ self.assertEqual(alns[0].sequences[0].name, 'A')
+ self.assertEqual(alns[0].sequences[1].name, 'B')
+ self.assertEqual(str(alns[0].sequences[0]), 'aacdefghiklmn')
+ self.assertEqual(str(alns[0].sequences[1]), '-acd---hiklmn')
+ self.assertEqual(alns[0].sequences[0].offset, 0)
+ self.assertEqual(alns[0].sequences[1].offset, 0)
+
+ def testDeletionInSeqA(self):
+ seq_a=seq.CreateSequence('A', 'acdhiklmn')
+ seq_b=seq.CreateSequence('B', 'acdefghiklmn')
+ alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
+ self.assertEqual(len(alns), 1)
+ self.assertEqual(alns[0].sequences[0].name, 'A')
+ self.assertEqual(alns[0].sequences[1].name, 'B')
+
+ self.assertEqual(str(alns[0].sequences[0]), 'acd---hiklmn')
+ self.assertEqual(str(alns[0].sequences[1]), 'acdefghiklmn')
+ self.assertEqual(alns[0].sequences[0].offset, 0)
+ self.assertEqual(alns[0].sequences[1].offset, 0)
+
+ def testOffset(self):
+ seq_a=seq.CreateSequence('A', 'acdhiklmn')
+ seq_b=seq.CreateSequence('B', 'ggiklmn')
+ alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
+ self.assertEqual(len(alns), 1)
+ self.assertEqual(alns[0].sequences[0].name, 'A')
+ self.assertEqual(alns[0].sequences[1].name, 'B')
+
+ self.assertEqual(str(alns[0].sequences[0]), 'acdhiklmn')
+ self.assertEqual(str(alns[0].sequences[1]), 'g--giklmn')
+ self.assertEqual(alns[0].sequences[0].offset, 0)
+ self.assertEqual(alns[0].sequences[1].offset, 0)
+
+if __name__ == "__main__":
+ try:
+ unittest.main()
+ except Exception, e:
+ print e
--
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