用于通用序列对齐的本机python库。
alignment的Python项目详细描述
alignment是通用序列对齐的本地python库。它是 在字母表任意大而不能使用 传统的生物序列分析工具。它支持全球和本地 成对序列对齐。我还计划添加对配置文件的支持 但谁知道什么时候。
安装
您可以使用pip:
pip install alignment
用法
典型用法如下：
from alignment.sequence import Sequence
from alignment.vocabulary import Vocabulary
from alignment.sequencealigner import SimpleScoring, GlobalSequenceAligner
# Create sequences to be aligned.
a = Sequence('what a beautiful day'.split())
b = Sequence('what a disappointingly bad day'.split())
# Create a vocabulary and encode the sequences.
v = Vocabulary()
aEncoded = v.encodeSequence(a)
bEncoded = v.encodeSequence(b)
# Create a scoring and align the sequences using global aligner.
scoring = SimpleScoring(2, -1)
aligner = GlobalSequenceAligner(scoring, -2)
score, encodeds = aligner.align(aEncoded, bEncoded, backtrace=True)
# Iterate over optimal alignments and print them.
for encoded in encodeds:
alignment = v.decodeSequenceAlignment(encoded)
print alignment
print 'Alignment score:', alignment.score
print 'Percent identity:', alignment.percentIdentity()
print
待办事项列表
- 纵断面纵断面对齐尚未工作。
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