Author: bugman
Date: Thu Jan 29 13:34:38 2015
New Revision: 27349
URL: http://svn.gna.org/viewcvs/relax?rev=27349&view=rev
Log:
Added the lib.sequence_alignment.align_protein.align_multiple_from_pairwise()
function.
This should have been committed earlier. The function is only partly
implemented.
Modified:
trunk/lib/sequence_alignment/align_protein.py
Modified: trunk/lib/sequence_alignment/align_protein.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/align_protein.py?rev=27349&r1=27348&r2=27349&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/align_protein.py (original)
+++ trunk/lib/sequence_alignment/align_protein.py Thu Jan 29 13:34:38 2015
@@ -23,12 +23,106 @@
"""General sequence alignment functions."""
# Python module imports.
+from numpy import int16, zeros
import sys
# relax module imports.
from lib.errors import RelaxError
from lib.sequence_alignment.needleman_wunsch import needleman_wunsch_align
from lib.sequence_alignment.substitution_matrices import BLOSUM62,
BLOSUM62_SEQ, PAM250, PAM250_SEQ
+
+
+def align_multiple_from_pairwise(reference_sequence, sequences,
algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0,
gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0):
+ """Align multiple protein sequences to one reference by fusing multiple
pairwise alignments.
+
+ @param reference_sequence: The first protein sequence as one
letter codes to use as the reference.
+ @type reference_sequence: str
+ @param sequences: The list of remaining protein
sequences as one letter codes.
+ @type sequences: list of str
+ @keyword algorithm: The pairwise sequence alignment
algorithm to use.
+ @type algorithm: str
+ @keyword matrix: The substitution matrix to use.
+ @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: The two alignment strings and the gap
matrix.
+ @rtype: str, str, numpy rank-2 int array
+ """
+
+ # The pairwise alignments.
+ N = len(sequences)
+ align1_list = []
+ align2_list = []
+ gap_list = []
+ for i in range(N):
+ # Pairwise alignment.
+ align1, align2, gaps = align_pairwise(reference_sequence,
sequences[i], algorithm=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)
+
+ # Store the results.
+ align1_list.append(align1)
+ align2_list.append(align2)
+ gap_list.append(gaps)
+
+ # Convert all sequence strings to lists.
+ ref_list = list(reference_sequence)
+ seq_list = []
+ for i in range(N):
+ seq_list.append(list(sequences[i]))
+
+ # Loop over the alignment elements.
+ strings = []
+ index = -1
+ offsets = zeros(N, int16)
+ while 1:
+ # Increment the index.
+ index += 1
+ print "\nIndex %i" % index
+
+ # Termination condition.
+ term = True
+ for i in range(N):
+ if index + offsets[i] < len(gap_list[i][0]):
+ term = False
+ else:
+ print " At end in %i" % i
+ if term:
+ break
+
+ # A gap in one of the references.
+ gap = False
+ for i in range(N):
+ if index + offsets[i] >= len(gap_list[i][0]) or gap_list[i][0,
index]:
+ print " Gap in %i" % i
+ offsets[i] += 1
+ gap = True
+ print " New offsets %s" % offsets
+
+ # No reference gap.
+ if not gap:
+ print " No ref gap."
+ continue
+
+ # Insert the gap into the reference list.
+ print " Inserting gap into ref list at %i" % index
+ ref_list.insert(index, '-')
+
+ for i in range(N):
+ seq = ''.join(seq_list[i])
+ strings.append(seq)
+
+ ref = ''.join(ref_list)
+
+ print ref_list
+ print seq_list
+
+ # Return the results.
+ return [ref] + strings, gap_list
def align_pairwise(sequence1, sequence2, algorithm='NW70', matrix='BLOSUM62',
gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0):
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