Author: bugman
Date: Fri Jan 30 11:58:44 2015
New Revision: 27387
URL: http://svn.gna.org/viewcvs/relax?rev=27387&view=rev
Log:
Implemented the data_store.seq_align.Sequence_alignments.find_alignment()
method.
This will only return an alignment if all alignment input data and alignment
settings match exactly.
Modified:
trunk/data_store/seq_align.py
Modified: trunk/data_store/seq_align.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/data_store/seq_align.py?rev=27387&r1=27386&r2=27387&view=diff
==============================================================================
--- trunk/data_store/seq_align.py (original)
+++ trunk/data_store/seq_align.py Fri Jan 30 11:58:44 2015
@@ -65,6 +65,80 @@
self.append(Alignment(object_ids=object_ids, molecules=molecules,
models=models, sequences=sequences, strings=strings, gaps=gaps,
msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm,
matrix=matrix, gap_open_penalty=gap_open_penalty,
gap_extend_penalty=gap_extend_penalty,
end_gap_open_penalty=end_gap_open_penalty,
end_gap_extend_penalty=end_gap_extend_penalty))
+ def find_alignment(self, object_ids=None, models=None, molecules=None,
sequences=None, msa_algorithm=None, pairwise_algorithm=None, matrix=None,
gap_open_penalty=None, gap_extend_penalty=None, end_gap_open_penalty=None,
end_gap_extend_penalty=None):
+ """Find any pre-existing sequence alignment.
+
+ @keyword object_ids: The list of IDs for each
structural object in the alignment. In most cases this will be the data pipe
name. This will be used to retrieve alignments.
+ @type object_ids: list of str
+ @keyword models: The list of model numbers used in
the alignment. This will be used to retrieve alignments.
+ @type models: list of int
+ @keyword molecules: The list of molecules used in the
alignment. This will be used to retrieve alignments.
+ @type molecules: list of str
+ @keyword sequences: The list of residue sequences for
the alignment as one letter codes.
+ @type sequences: list of str
+ @keyword msa_algorithm: The global multiple sequence
alignment (MSA) algorithm.
+ @type msa_algorithm: str
+ @keyword pairwise_algorithm: The pairwise sequence alignment
algorithm.
+ @type pairwise_algorithm: str
+ @keyword matrix: The substitution matrix
+ @type matrix: str
+ @keyword gap_open_penalty: The penalty for introducing gaps,
as a positive number.
+ @type gap_open_penalty: float
+ @keyword gap_extend_penalty: The penalty for extending a gap,
as a positive number.
+ @type gap_extend_penalty: float
+ @keyword end_gap_open_penalty: The optional penalty for opening a
gap at the end of a sequence.
+ @type end_gap_open_penalty: float
+ @keyword end_gap_extend_penalty: The optional penalty for extending
a gap at the end of a sequence.
+ @type end_gap_extend_penalty: float
+ @return: Any matching sequence alignment
object.
+ @rtype: Alignment instance
+ """
+
+ # Loop over all current alignments.
+ for i in range(len(self)):
+ # Starting flag.
+ found = True
+
+ # Loop over the molecules.
+ for j in range(len(object_ids)):
+ # Check for any mismatches (breaking the loop for speed by
avoiding unnecessary checks).
+ if self[i].object_ids[j] != object_ids[j]:
+ found = False
+ break
+ if self[i].models[j] != models[j]:
+ found = False
+ break
+ if self[i].molecules[j] != molecules[j]:
+ found = False
+ break
+ if self[i].sequences[j] != sequences[j]:
+ found = False
+ break
+
+ # No match (skip the rest of the checks for speed).
+ if not found:
+ continue
+
+ # Check the alignment settings for mismatches.
+ if self[i].msa_algorithm != msa_algorithm:
+ continue
+ if self[i].pairwise_algorithm != pairwise_algorithm:
+ continue
+ if self[i].matrix != matrix:
+ continue
+ if self[i].gap_open_penalty != gap_open_penalty:
+ continue
+ if self[i].gap_extend_penalty != gap_extend_penalty:
+ continue
+ if self[i].end_gap_open_penalty != end_gap_open_penalty:
+ continue
+ if self[i].end_gap_extend_penalty != end_gap_extend_penalty:
+ continue
+
+ # No mismatches, so this must be the alignment.
+ return self[i]
+
+
class Alignment(Element):
"""Container for an individual sequence alignment."""
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