Author: bugman Date: Thu Jan 22 17:21:34 2015 New Revision: 27276 URL: http://svn.gna.org/viewcvs/relax?rev=27276&view=rev Log: Added the end gap penalty arguments to lib.sequence_alignment.align_protein.align_pairwise().
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=27276&r1=27275&r2=27276&view=diff ============================================================================== --- trunk/lib/sequence_alignment/align_protein.py (original) +++ trunk/lib/sequence_alignment/align_protein.py Thu Jan 22 17:21:34 2015 @@ -32,23 +32,27 @@ from lib.sequence_alignment.substitution_matrices import BLOSUM62, BLOSUM62_SEQ -def align_pairwise(sequence1, sequence2, algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0, gap_extend_penalty=1.0): +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): """Align two protein sequences. - @param sequence1: The first protein sequence as one letter codes. - @type sequence1: str - @param sequence2: The second protein sequence as one letter codes. - @type sequence2: str - @keyword algorithm: The 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 - @return: The two alignment strings and the gap matrix. - @rtype: str, str, numpy rank-2 int array + @param sequence1: The first protein sequence as one letter codes. + @type sequence1: str + @param sequence2: The second protein sequence as one letter codes. + @type sequence2: str + @keyword algorithm: The 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 """ # Checks. @@ -78,7 +82,7 @@ # The alignment. if algorithm == 'NW70': - 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) + 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)) _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits