Author: bugman
Date: Thu Jan 29 14:16:23 2015
New Revision: 27352
URL: http://svn.gna.org/viewcvs/relax?rev=27352&view=rev
Log:
Added the verbosity argument to
lib.sequence_alignment.align_protein.align_pairwise().
If set to zero, all printouts are suppressed.
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=27352&r1=27351&r2=27352&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/align_protein.py (original)
+++ trunk/lib/sequence_alignment/align_protein.py Thu Jan 29 14:16:23 2015
@@ -31,7 +31,7 @@
from lib.sequence_alignment.substitution_matrices import BLOSUM62,
BLOSUM62_SEQ, PAM250, PAM250_SEQ
-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):
+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, verbosity=1):
"""Align two protein sequences.
@param sequence1: The first protein sequence as one
letter codes.
@@ -50,6 +50,8 @@
@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
+ @keyword verbosity: The level of verbosity. Setting this
to zero silences all printouts.
+ @type verbosity: int
@return: The two alignment strings and the gap
matrix.
@rtype: str, str, numpy rank-2 int array
"""
@@ -67,12 +69,13 @@
sequence2 = sequence2.upper()
# Initial printout.
- sys.stdout.write("\nPairwise protein alignment.\n")
- sys.stdout.write("%-30s %s\n" % ("Substitution matrix:", matrix))
- sys.stdout.write("%-30s %s\n" % ("Gap opening penalty:", gap_open_penalty))
- sys.stdout.write("%-30s %s\n" % ("Gap extend penalty:",
gap_extend_penalty))
- sys.stdout.write("\n%-30s %s\n" % ("Input sequence 1:", sequence1))
- sys.stdout.write("%-30s %s\n" % ("Input sequence 2:", sequence2))
+ if verbosity:
+ sys.stdout.write("\nPairwise protein alignment.\n")
+ sys.stdout.write("%-30s %s\n" % ("Substitution matrix:", matrix))
+ sys.stdout.write("%-30s %s\n" % ("Gap opening penalty:",
gap_open_penalty))
+ sys.stdout.write("%-30s %s\n" % ("Gap extend penalty:",
gap_extend_penalty))
+ sys.stdout.write("\n%-30s %s\n" % ("Input sequence 1:", sequence1))
+ sys.stdout.write("%-30s %s\n" % ("Input sequence 2:", sequence2))
# Select the substitution matrix.
if matrix == 'BLOSUM62':
@@ -87,15 +90,16 @@
align1, align2, gaps = needleman_wunsch_align(sequence1, sequence2,
sub_matrix=sub_matrix, sub_seq=sub_seq, 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)
# Final printout.
- sys.stdout.write("\n%-30s %s\n" % ("Aligned sequence 1:", align1))
- sys.stdout.write("%-30s %s\n" % ("Aligned sequence 2:", align2))
- sys.stdout.write("%-30s " % "")
- for i in range(len(align1)):
- if align1[i] == align2[i]:
- sys.stdout.write("*")
- else:
- sys.stdout.write(" ")
- sys.stdout.write("\n\n")
+ if verbosity:
+ sys.stdout.write("\n%-30s %s\n" % ("Aligned sequence 1:", align1))
+ sys.stdout.write("%-30s %s\n" % ("Aligned sequence 2:", align2))
+ sys.stdout.write("%-30s " % "")
+ for i in range(len(align1)):
+ if align1[i] == align2[i]:
+ sys.stdout.write("*")
+ else:
+ sys.stdout.write(" ")
+ sys.stdout.write("\n\n")
# Return the results.
return align1, align2, gaps
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