分析拼接接头的python程序
junc-utils的Python项目详细描述
接合处
分析拼接接头的实用功能(由star、.sj.out.tab文件生成)
依赖性
Python
pysam,annot_utils包
软件
安装
pip install junc_utils
或者,也可以从源代码安装
wget https://github.com/friend1ws/junc_utils/archive/v0.4.0.tar.gz
tar zxvf v0.4.0.tar.gz
cd junc_utils-0.4.0
python setup.py build install
这个包已经在Python2.7、3.5、3.6上测试过了。
命令
菲特勒
过滤掉指定条件外的拼接接头
junc_utils filter [-h] [--read_num_thres READ_NUM_THRES]
[--overhang_thres OVERHANG_THRES] [--keep_annotated]
[--pooled_control_file POOLED_CONTROL_FILE]
sample.SJ.out.tab output.txt
注释
注释拼接接头
junc_utils annotate [-h] [--grc] [--genome_id {hg19,hg38,mm10}]
[--junction_margin JUNCTION_MARGIN]
[--exon_margin EXON_MARGIN]
sample.SJ.out.tab output.txt
合并控件
合并、压缩并索引拼接连接列表
junc_utils merge_control [-h] [--read_num_thres READ_NUM_THRES]
[--overhang_thres OVERHANG_THRES]
[--keep_annotated]
[--sample_num_thres SAMPLE_NUM_THRES]
junc_list.txt output_path
关联
将连接与突变或svs联系起来
junc_utils associate [-h] [--grc] [--genome_id {hg19,hg38,mm10}]
[--donor_size donor_size]
[--acceptor_size acceptor_size]
[--reference reference.fa] [--debug]
[--mutation_format {vcf,anno}] [--only_dist]
[--only_dist_search_margin only_dist_search_margin]
[--sv] [--branchpoint]
[--branchpoint_size branchpoint_size]
annotated_junction.SJ.out.tab mutation.vcf.gz
output_file