Metadata-Version: 2.1
Name: famCircle
Version: 0.1.5
Summary: famCircle
Home-page: UNKNOWN
Author: charles_kiko
Author-email: charles_kiko@163.com
License: BSD License
Description: # famCircle 基因家族分析，tandem可视化分析
        
        ## 分析流程
        
        基因组下载以及处理
        	路线1：
        		ks展示
        		hmmer搜索筛选
        			断开处：
        				pfam结构域筛选
        				α/β筛选
        		主程序选择：
        			inner
        			outer
        	路线2：
        		blast、共线性文件筛选
        		主程序选择：
        			inner
        			outer
        
        ## ks分布可视化
        run ks
        ks = ks file
        vertical = False
        bins = 100
        model = YN00/NG86
        savefile = save file (*.png, *.pdf)
        
        ## 结构域分布情况
        run screen
        domainpath = domain file
        lens = lens file
        gff = gff file
        chrolist = Genome name
        series = 25
        outpath = out file
        
        ## 基因家族查找
        run hmmer 
        pep = pep file# 蛋白质文件
        hmmmoldpath = hmm file# 模型地址
        format_conversion = Fales# 格式转换
        comparison = muscle/clustal# 比对软件
        e_value1 = value1
        e_value2 = value2
        
        ## 结构域筛选
        
        ## α/β筛选
        
        ## 内卷型的tandem可视化
        run inner
        lens = lens file
        gff = gff file
        chrolist = Genome name
        ks = ks file
        genefamily = famliy file
        Ks_concern = 0.1,0.2,1.4,1.5# ks分割参数可调
        bridge = 0.05# 最远连接
        radius = 0.3
        peripheral = False
        savecsv = outer file (*.csv)
        savefile = save file (*.png, *.pdf)
        
        ## 共线性可视化
        run circle
        lens = lens file
        gff = gff file
        chrolist = Genome name
        ks = ks file
        genepairs = genepairs file
        peripheral = False
        block = 6
        Ks_concern = 0,0.15
        bridge = 1
        radius = 0.3
        savefile = save file (*.png, *.pdf)
        
        ## 放射型的tandem可视化
        run outer
        lens = lens file
        gff = gff file
        chrolist = Genome name
        ks = ks file
        genepairs = genepairs file
        Ks_concern = 0,0.15# ks分割参数可调
        series = 25# 串联数
        clusters = None# 集团参数可调
        peripheral = False
        bridge = 1# 跨区域连线参数可调
        radius = 0.3
        savecsv = outer file (*.csv)
        savefile = save file (*.png, *.pdf)
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
