ngstools
Project description
Author : Liubo <Ben-unbelieveable>
ngstools
Useful toolkits for NGS analysis
Main Class
CPRA
一个最简化的突变对象，通过染色体位置完成对象的初始化，同时支持加载参考基因组和样本比对的Bam文件，来实现更多的个性化操作。
from ngstoolkits import CPRA
# 初始化对象
mutsite=CPRA("chr6",159188398,"C","T")
# 加载bam文件
CPRA.loadBam("test_data/pancancer689__DX2083_sijuan_20S12590085_20B12590085__Cancer.realign.bam")
# 加载参考基因组
CPRA.loadReference("test_data/hg19.fa")
# 基于Bam文件获取突变支持信息
mutsite.get_suppot()
# 得到的突变支持信息
mutsite.support_reads # 支持突变的list，内容是pysam的AlignedSegment对象
mutsite.cover_readsID_list # 支持突变的reads的ID
mutsite.support_readsID_list # 覆盖突变的reads的ID
Seq
序列处理相关的静态函数
Seq.reverse_complement
返回所提供序列的反向互补序列
from ngstoolkits import Seq
Seq.reverse_complement("ATGC") # 返回 "GCAT"
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