Closed PAXMANXN closed 4 months ago
Xin chào bạn,
from skbio.alignment import local_pairwise_align_ssw
from skbio.alignment import StripedSmithWaterman
from skbio import TabularMSA, DNA
# StripedSmithWaterman local pairwise alignment
alignment, score, start_end_pos = local_pairwise_align_ssw(
DNA("ACTAAGGCTCTCTACCCCTCTCAGAGA"),
DNA("ACTAAGGCTCCTAACCCCCTTTTCTCAGA")
)
print(alignment)
print(score)
print(start_end_pos)
print("")
# SSW object
query = StripedSmithWaterman("ACTAAGGCTCTCTACCCCTCTCAGAGA")
alignment = query("AAAAAACTCTCTAAACTCACTAAGGCTCTCTACCCCTCTTCAGAGAAGTCGA")
print(f"Optimal alignment score: {alignment.optimal_alignment_score}")
print(f"Cigar string: {alignment.cigar}")
print(f"Query sequence: {alignment.aligned_query_sequence}")
print(f"Target sequence: {alignment.aligned_target_sequence}")
TabularMSA[DNA]
------------------------------
Stats:
sequence count: 2
position count: 30
------------------------------
ACTAAGGCTCTCT-ACCCC----TCTCAGA
ACTAAGGCTC-CTAACCCCCTTTTCTCAGA
27
[(0, 24), (0, 28)]
Optimal alignment score: 49
Cigar string: 20M1D7M
Query sequence: ACTAAGGCTCTCTACCCCTC-TCAGAGA
Target sequence: ACTAAGGCTCTCTACCCCTCTTCAGAGA
- Zhao, Mengyao, Wan-Ping Lee, Erik P. Garrison, & Gabor T. Marth. “SSW Library: An SIMD Smith-Waterman C/C++ Library for Applications”. PLOS ONE (2013). Web. 11 July 2014. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082138
- scikit-bio/scikit-bio: scikit-bio, Version 0.6.0 10.5281/zenodo.10888788
Cảm ơn bạn Đức Minh rất nhiều !
Nếu bạn không có thắc mắc gì thêm, minh sẽ close issue này. Nếu bất kỳ anh/chị/bạn nào có thắc mắc có thể thoải mái open issue này lại. Mình cám ơn.
Hi các bạn, các trình tự khác nhau về chiều dài DNA thì có làm alginment theo các syntax dưới không?