From ad7b23aec528c43fa68cd7976dcfa65e772d6c9c Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Fri, 24 Jun 2016 13:56:45 +0200
Subject: [PATCH] fixed Renumber-function which was failing for the given
example code
---
modules/seq/alg/doc/seqalg.rst | 1 +
modules/seq/alg/pymod/renumber.py | 65 +++++++++++++++++++------------
2 files changed, 41 insertions(+), 25 deletions(-)
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index 5b70b99fc..0285d04c7 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -163,6 +163,7 @@ Algorithms for Alignments
:param gap_ext: The gap extension penalty. Must be a negative number
:returns: best-scoring alignment of *seq1* and *seq2*.
+.. autofunction:: ost.seq.alg.renumber.Renumber
.. _contact-prediction:
diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
index 22873111e..899ad1e16 100644
--- a/modules/seq/alg/pymod/renumber.py
+++ b/modules/seq/alg/pymod/renumber.py
@@ -1,6 +1,4 @@
-from ost import io, seq, mol, conop
-from ost import *
-
+from ost import seq, mol
def _RenumberSeq(seq_handle):
if not seq_handle.HasAttachedView():
@@ -8,14 +6,13 @@ def _RenumberSeq(seq_handle):
ev = seq_handle.attached_view.CreateEmptyView()
new_numbers = mol.ResNumList()
for pos in range(len(seq_handle)):
- if seq_handle[pos]!='-':
- r=seq_handle.GetResidue(pos)
+ if seq_handle[pos] != '-':
+ r = seq_handle.GetResidue(pos)
if r.IsValid():
- #print seq_handle[pos],r.number.num,pos+1
ev.AddResidue(r, mol.INCLUDE_ALL)
new_numbers.append(pos+1)
else:
- raise RuntimeError('Error: renumbering failed at position %s' %pos)
+ raise RuntimeError('Error: renumbering failed at position %s' % pos)
return ev, new_numbers
def _RenumberAln(aln, seq_index):
@@ -25,44 +22,62 @@ def _RenumberAln(aln, seq_index):
ev = aln.sequences[seq_index].attached_view.CreateEmptyView()
new_numbers = mol.ResNumList()
for col in aln:
- if col[0]!='-' and col[seq_index]!='-':
- if col[0]!=col[seq_index]:
- raise RuntimeError("residue mismatch at position %d (%s vs %s) (renumbering failed)"%(counter, col[0],col[1]))
- rnum=aln.GetSequence(seq_index).GetResidueIndex(counter)
- r=aln.GetSequence(seq_index).GetResidue(counter)
+ if col[0] != '-' and col[seq_index] != '-':
+ if col[0] != col[seq_index]:
+ raise RuntimeError("residue mismatch at position %d (%s vs %s) "\
+ "(renumbering failed)" % (counter, col[0],
+ col[seq_index]))
+ rnum = aln.GetSequence(seq_index).GetResidueIndex(counter)
+ r = aln.GetSequence(seq_index).GetResidue(counter)
if not r.IsValid():
- raise RuntimeError("invalid residue at postion %s (renumbering failed)" %(counter))
+ raise RuntimeError("invalid residue at postion %s (renumbering failed)"\
+ % (counter))
ev.AddResidue(r, mol.INCLUDE_ALL)
new_numbers.append(counter+1)
- counter+=1
+ counter += 1
return ev, new_numbers
def Renumber(seq_handle, sequence_number_with_attached_view=1):
"""
- Function to renumber an entity according to an alignment between the model sequence
- and the full-length target sequence. The aligned model sequence or the alignment itself
- with an attached view needs to be provided. Upon succcess, the renumbered entity is returned.
+ Function to renumber an entity according to an alignment between the model
+ sequence and the full-length target sequence. The aligned model sequence or
+ the alignment itself with an attached view needs to be provided. Upon
+ succcess, the renumbered entity is returned.
+ If an alignment is given, the sequence must
.. code-block:: python
from ost.seq.alg import renumber
from ost.bindings.clustalw import *
- ent=io.LoadPDB("path_to_model")
- s=io.LoadSequence("path_to_full_length_fasta_seqeunce")
- pdb_seq=seq.SequenceFromChain("model", ent.chains[0])
- aln=ClustalW(s,pdb_seq)
- aln.AttachView(1,ent.chains[0].Select(""))
- e=Renumber(aln.GetSequence(sequence_number_with_attached_view))
+ ent = io.LoadPDB("path_to_model")
+ s = io.LoadSequence("path_to_full_length_fasta_seqeunce")
+ pdb_seq = seq.SequenceFromChain("model", ent.chains[0])
+ aln = ClustalW(s, pdb_seq)
+ aln.AttachView(1, ent.chains[0].Select(""))
+ e = Renumber(aln.sequences[1])
io.SavePDB(e, "renum.pdb")
+ :param seq_handle: Sequence or alignment handle with attached view.
+ :type seq_handle: :class:`SequenceHandle` / :class:`AlignmentHandle`
+ :param sequence_number_with_attached_view: Sequence number for the aln. handle
+ (not used if seq. handle given)
+ :type sequence_number_with_attached_view: :class:`int`
+ :raises: :exc:`RuntimeError` if unknown type of *seq_handle* or if attached
+ view is missing or if the given alignment sequence is inconsistent.
"""
- if isinstance(seq_handle, seq.SequenceHandle):
+ if isinstance(seq_handle, seq.SequenceHandle) \
+ or isinstance(seq_handle, seq.ConstSequenceHandle):
ev, new_numbers = _RenumberSeq(seq_handle)
elif isinstance(seq_handle, seq.AlignmentHandle):
ev, new_numbers = _RenumberAln(seq_handle, sequence_number_with_attached_view)
+ else:
+ raise RuntimeError("Unknown input type " + str(type(seq_handle)))
ev.AddAllInclusiveBonds()
- new_ent = mol.CreateEntityFromView(ev,False);
+ new_ent = mol.CreateEntityFromView(ev, False);
new_ent.EditXCS().RenumberChain(new_ent.chains[0], new_numbers)
return new_ent
+
+# choose visible interface
+__all__ = ('Renumber', )
\ No newline at end of file
--
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