Comments (4)
Thanks for the bug report. I just pushed a fixed for this, and added your example to the unit tests. I moved the match
and mismatch
scores to the Matrix class. If you wish to customize your match
and mismatch
values, you can create your own Matrix
instance, and pass it as part of the Aligner
constructor. In the future, I intend to add more support for ambiguity bases and protein alignments, which is why I broke the Matrix
into its own class.
from ssw.
Thank you, this solves a big part of my problem. Here is the new output
>>> print(alignment.alignment_report())
Score = 40, Matches = 29, Mismatches = 9, Insertions = 0, Deletions = 0
ref 4 AGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAG
||*|||*|||*|||*|||*|||*|||*|||*|||*|||
query 1 AGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAG
It seems like the last two characters are cut from this alignment, probably because they contain one mismatch and one match so the score is 0 for these two last characters --- and one alignment is returned. I thought I can solve it by letting e.g. mismatch = -1 and match =1. I issued:
>>> score_matrix = ssw.ScoreMatrix(match=2,mismatch=-1)
>>> aligner = ssw.Aligner(ref_seq, matrix=score_matrix, gap_open=1, gap_extend=1)
>>> alignment = aligner.align(query_seq)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/kxs624/.pyenv/versions/2.7.9/lib/python2.7/site-packages/ssw/sswobj.py", line 95, in align
res = self._align(query, reference, flags, filter_score, filter_distance, mask_length)
File "/Users/kxs624/.pyenv/versions/2.7.9/lib/python2.7/site-packages/ssw/sswobj.py", line 104, in _align
_query = self.matrix.convert_sequence_to_ints(query)
File "/Users/kxs624/.pyenv/versions/2.7.9/lib/python2.7/site-packages/ssw/sswobj.py", line 62, in convert_sequence_to_ints
return _seq_type(*seq_generator)
File "/Users/kxs624/.pyenv/versions/2.7.9/lib/python2.7/site-packages/ssw/sswobj.py", line 61, in <genexpr>
seq_generator = (self.symbol_map[symbol.upper()] for symbol in seq)
KeyError: 'A'
from ssw.
The problem is that you need to use the DNA_ScoreMatrix
, since ScoreMatrix
has no alphabet
defined.
reference = "CCC" + "AGCT" * 10
query = "AGGT" * 10
score_matrix = ssw.DNA_ScoreMatrix(match=2, mismatch=-1)
aligner = ssw.Aligner(matrix=score_matrix)
alignment = aligner.align(query, reference)
print(alignment.alignment_report())
Score = 50, Matches = 30, Mismatches = 10, Insertions = 0, Deletions = 0
ref 4 AGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCT
||*|||*|||*|||*|||*|||*|||*|||*|||*|||*|
query 1 AGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGT
from ssw.
Thank you, that solves it!
from ssw.
Related Issues (8)
- Key Error in sswobj.py
- Consider uploading ssw to PyPi? HOT 2
- Segmentation fault 11 HOT 2
- Speed enhancement HOT 8
- Include some more examples with other features in the README? (Enhancement)
- How are gaps to be represented (formating) in the strings? ('-' creates an error)
- error LNK2001: unresolved external symbol pyinit_libssw
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from ssw.