famCircle 0.2.5
famCircle
License: BSD License

# 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