在python中快速读取和操作多个序列对齐
alignmentrs的Python项目详细描述
对齐器
在python中快速读取和操作多个序列对齐
安装
pip install alignmentrs
快速启动
将对齐导入python
>>>importalignmentrsasrs>>>aln=rs.Alignment.from_fasta('hiv.fna','HIV_alignment')>>>alnAlignment(nsamples=10,nsites=120,nmarkers=0)>>>aln.sample_ids['sample01','sample02','sample03','sample04','sample05','sample06''sample07','sample08','sample09','sample10']
选择要从路线中删除的站点
>>>sites_to_remove=[iforiinrange(120)if(i-2)%3!=0]# remove 1st and 2nd position in codon triplet>>>aln.remove_sites(sites_to_remove,copy=False)# manipulate inplace, copy=True returns a new copyAlignment(nsamples=10,nsites=40,nmarkers=0)
选择要在路线中保留的站点
>>>sites_to_retain=list(range(2,3,120))# third position in codon triplet>>>aln.retain_sites(sites_to_retain,copy=False)# manipulate inplace, copy=True returns a new copyAlignment(nsamples=10,nsites=40,nmarkers=0)
获取样本和站点的子集
>>>sub_aln=aln.subset(samples=['sample01','sample03','sample05'],sites=list(range(2,3,120)))>>>sub_alnAlignment(nsamples=3,nsites=40,nmarkers=0)
许可证
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