From abba7e6e2561fe056d1c8ef8b4498b5be8a2b067 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 15 Apr 2010 09:31:34 +0000
Subject: [PATCH] clustalw bindings
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2014 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/CMakeLists.txt | 3 +-
modules/bindings/pymod/clustalw.py | 22 +++++++++++++
modules/bindings/pymod/utils.py | 47 +++++++++++++++++++++++++++
3 files changed, 71 insertions(+), 1 deletion(-)
create mode 100644 modules/bindings/pymod/clustalw.py
create mode 100644 modules/bindings/pymod/utils.py
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index c17cb439f..86fad8a93 100644
--- a/modules/bindings/pymod/CMakeLists.txt
+++ b/modules/bindings/pymod/CMakeLists.txt
@@ -1 +1,2 @@
-pymod(NAME bindings PY __init__.py lga.py hbplus.py msms.py tmtools.py dssp.py)
+pymod(NAME bindings PY __init__.py lga.py hbplus.py msms.py tmtools.py
+ dssp.py clustalw.py utils.py)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
new file mode 100644
index 000000000..3625ede81
--- /dev/null
+++ b/modules/bindings/pymod/clustalw.py
@@ -0,0 +1,22 @@
+from ost.bindings import utils
+from ost import settings, io, seq
+import os
+import subprocess
+
+def ClustalW(seq1, seq2, clustalw=None):
+ clustalw_path=settings.Locate(('clustalw', 'clustalw2'),
+ explicit_file_name=clustalw)
+ seq_list=seq.CreateSequenceList()
+ seq_list.AddSequence(seq1)
+ seq_list.AddSequence(seq2)
+ temp_dir=utils.TempDirWithFiles((seq_list,))
+ out=os.path.join(temp_dir.dirname, 'out.fasta')
+ command='%s -infile="%s" -output=fasta -outfile="%s"' % (clustalw_path,
+ temp_dir.files[0],
+ out)
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ ps.stdout.readlines()
+ aln=io.LoadAlignment(out)
+ temp_dir.Cleanup()
+ return aln
+
\ No newline at end of file
diff --git a/modules/bindings/pymod/utils.py b/modules/bindings/pymod/utils.py
new file mode 100644
index 000000000..27d4008d8
--- /dev/null
+++ b/modules/bindings/pymod/utils.py
@@ -0,0 +1,47 @@
+import os
+from ost import seq, mol, io
+import tempfile
+def SaveToTempDir(objects, seq_format='fasta', structure_format='pdb'):
+ """
+ Take all objects and saves them to a temporary directory. The paths of the
+ saved files will be returned as a tuple. This works for alignments, and
+ structure files. The output format for sequence files and structure files can
+ be changed by setting to seq_format and structure_format parameters
+ appropriately.
+ """
+ # create temporary directory
+ tmp_dir_name=tempfile.mkdtemp()
+ file_names=[]
+ for index, obj in enumerate(objects):
+ if isinstance(obj, seq.AlignmentHandle):
+ name=os.path.join(tmp_dir_name, 'aln%02d.fasta' % (index+1))
+ io.SaveAlignment(obj, name, seq_format)
+ file_names.append(name)
+ continue
+ if isinstance(obj, seq.SequenceHandle):
+ name=os.path.join(tmp_dir_name, 'seq%02d.fasta' % (index+1))
+ io.SaveSequence(obj, name, seq_format)
+ file_names.append(name)
+ continue
+ if isinstance(obj, seq.ConstSequenceList) or isinstance(obj, seq.SequenceList):
+ name=os.path.join(tmp_dir_name, 'sql%02d.fasta' % (index+1))
+ io.SaveSequenceList(obj, name, seq_format)
+ file_names.append(name)
+ continue
+ if isinstance(obj, mol.EntityView) or isinstance(obj, mol.EntityHandle):
+ name=os.path.join(tmp_dir_name, tmp_dir_name, 'mol%02d.pdb' % (index+1))
+ io.SaveEntity(model, name, structure_format)
+ file_names.append(name)
+ continue
+ return file_names
+
+class TempDirWithFiles:
+ def __init__(self, objects, seq_format='fasta', structure_format='pdb'):
+ self.files=SaveToTempDir(objects, seq_format=seq_format,
+ structure_format=structure_format)
+ self.dirname=os.path.dirname(self.files[0])
+ def Cleanup(self):
+ import shutil
+ shutil.rmtree(self.dirname)
+
+
--
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