Metadata-Version: 2.1
Name: famCircle
Version: 0.2.4
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：
        		前期处理序列比对、共线性扫描、ks计算
        		ks展示
        			全基因组 ks展示
        			block ks展示
        		circle全基因组共线性展示
        		line局部共线性绘制
        		hmmer 隐马尔可夫模型搜索筛选
        		screen tandem数量分部
        			断开处：
        				pfam结构域筛选# http://pfam.xfam.org/
        				α/β筛选# http://cb.csail.mit.edu/cb/paircoil2/
        		主程序选择：
        			inner
        				typing 数据格式化
        				inner绘图
        			outer
        				typing 数据格式化
        				outer绘图
        		part局部tandem绘制
        
        # 配置文件解释
        
        ## 总体ks分布可视化
        run ks
        ks = ks file
        vertical = False
        bins = 100
        model = YN00/NG86
        savefile = save file (*.png, *.pdf)
        
        ## 基因块ks分布可视化
        run Ks_allocation
        ks = ks file
        area = 0,2
        vertical = False
        model = YN00/NG86
        blockfile = block file
        blocklength = 6
        pvalue = 0.05
        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)
        
        ## 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# 初筛阈值
        e_value2 = value2# 复筛阈值
        
        ## 结构域筛选
        ## α/β筛选
        
        ## 结构域分布情况
        run screen
        domainpath = domain file path
        lens = lens file
        gff = gff file
        chrolist = Genome name
        series = 25# 串联数
        outpath = out file path
        
        ## 文件格式化
        run typing
        domainpath = domain file# 文件路径
        domainlist = Genome name# 文件名列表
        position = inner/outer# 目标程序格式
        savefile = out file# 保存文件
        
        ## 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)
        
        ## 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)
        
        
        [circle]
        lens = lens file
        gff = gff file
        species_list = Genome name
        ks = ks file
        genepairs = genepairs file
        block = 6
        radius = 0.45
        savefile = save file (*.png, *.pdf)
        
        
        [circle_all]
        lens = lens file
        gff = gff file
        species_list = Genome name
        blockfile = block file
        radius = 0.3
        savefile = save file (*.png, *.pdf)
        
        
        [hmmer]
        pep = pep file
        cds = cds file
        hmmmoldpath = hmm file
        format_conversion = Fales
        comparison = clustal
        e_value1 = value1
        e_value2 = value2
        
        
        [inner]
        lens = lens file
        gff = gff file
        chrolist = Genome name
        ks = ks file
        genefamily = famliy file
        Ks_concern = 0,1.5
        radius = 0.3
        space = 0.005
        clusters = True
        peripheral = False
        savecsv = outer file (*.csv)
        savefile = save file (*.png, *.pdf)
        
        
        
        
        [Ks]
        cds_file = 	cds file
        pep_file = 	pep file
        align_software = muscle
        pairs_file = gene pairs file
        ks_file = ks result
        
        
        [Ks_allocation]
        ks = ks file
        species_list = specise name
        area = 0,2.5
        model = YN00/NG86
        savefile = save file (*.png, *.pdf)
        
        
        [Ks_block]
        species_list = specise name
        ks = ks file
        area = 0,2.5
        model = YN00/NG86
        blockfile = block file
        blocklength = 6
        pvalue = 1e-5
        savecsv = save csv
        savefile = save file (*.png, *.pdf)
        
        
        [line]
        pairs_file = pairs file
        gff1 =  gff1 file
        gff2 =  gff2 file
        lens1 = lens1 file
        lens2 = lens2 file
        chr1_name =  chr1 name
        chr2_name =  chr2 name
        savefile = savefile(.png,.pdf)
        
        
        [outer]
        lens = lens file
        gff = gff file
        chrolist = Genome name
        ks = ks file
        genefamily = famliy file
        Ks_concern = 0,0.15
        radius = 0.3
        space = 0.005
        clusters = True
        peripheral = False
        savecsv = outer file (*.csv)
        savefile = save file (*.png, *.pdf)
        
        
        [part]
        lens = lens file
        gff = gff file
        chrolist = Genome name
        ks = ks file
        genefamily = famliy file
        Ks_concern = 0,1.5
        radius = 0.3
        space = 0.005
        clusters = True
        peripheral = False
        savecsv = outer file (*.csv)
        savefile = save file (*.png, *.pdf)
        
        
        
        [screen]
        domainpath = domain file
        lens = lens file
        gff = gff file
        chrolist = Genome name
        series = 25
        outpath = out file
        
        
        [typing]
        domainpath = domain file
        domainlist = Genome name
        savefile = out file
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
