物种间共线性图

作者: 多啦A梦的时光机_648d | 来源:发表于2020-06-04 09:54 被阅读0次

    参考:
    https://blog.csdn.net/u012110870/article/details/102804593
    https://www.jianshu.com/p/1658e702ba17

    首先查看一下gff文件和CDS文件的对应情况,有的gff文件没有transcript_id这个注释。
    比如我的就没有

    python -m jcvi.formats.gff bed --type=mRNA --key=Name T_ant_maker.final.gff  > T.bed
    python -m jcvi.formats.gff bed --type=mRNA --key=Name A_aqu_genome.final.gff  > A.bed
    ···
    如果没有CDS文件,就自己提取
    gffread in.gff3 -g ref.fa -x cds.fa
    ···
    python -m jcvi.formats.fasta format --sep="|" T_ant_cds.fa T.cds
    python -m jcvi.formats.fasta format --sep="|" A_aQU_cds.fa A.cds
    
    python -m jcvi.compara.catalog ortholog T A --cscore=.99(画个点图看看共线性)
    
    python -m jcvi.compara.synteny screen --minspan=30 --simple T.A.anchors T.A.anchors.new
    或者不加参数:python -m jcvi.compara.synteny screen --simple T.A.anchors T.A.anchors.new
    python /home/spider/project/yuantao/script/hoptop_scripts/simple2links.py T.A.anchors.simple
    python /home/spider/project/yuantao/script/simple2links.py A.T.anchors.simple
    

    T.A.anchors.simple_link.txt文件就可因用来画圈图了,你也可以把里面每个染色体的共线性区块保存成一个文件,后面画不同的颜色。



    类似上图1号染色体的复制粘贴放一个文件,2号染色体的复制粘贴放一个文件,以此类推。

    circos.conf文件,每个染色体区块单独设置颜色。

    karyotype=karyotype.Aaqu.txt,karyotype.Tant.txt
    chromosomes_units = 100000
    
    <ideogram>
    <spacing>
    default = 0.005r
    <pairwise Aaqu01;Tant13>
    spacing = 6r
    </pairwise>
    </spacing>
    radius           = 0.90r
    thickness        = 6p
    fill             = yes
    stroke_color     = 160,32,240
    stroke_thickness = 2p
    show_bands = no
    show_label = yes
    label_font = default
    label_radius = dims(ideogram,radius) + 0.05r
    label_size = 9
    label_parallel = yes
    label_fromat = eval(sprintf("%s",var(chr)))
    </ideogram>
    
    <links>
        bezier_radius=0r
        bezier_radius_purity=0.75
        color=set2-8-qual-1
        crest=0.5   ##以上几列为links的全局的设置,包括连线的弯曲度,颜色
    <link>
    file = chr1_color.txt  ##1号染色体的共线性文件
    radius = 0.85r
    color = green_a2
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr2_color.txt  ##2号染色体的共线性文件
    radius = 0.85r
    color = red
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr3_color.txt   ##3号染色体的共线性文件
    radius = 0.85r
    color = purple
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr4_color.txt
    radius = 0.85r
    color = black
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr5_color.txt
    radius = 0.85r
    color = vvdblue
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr6_color.txt
    radius = 0.85r
    color = orange
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    
    <link>
    file = chr7_color.txt
    radius = 0.85r
    color = vvdpurple
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr8_color.txt
    radius = 0.85r
    color = vvdred
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr9_color.txt
    radius = 0.85r
    color =     255,255,0
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr10_color.txt
    radius = 0.85r
    color =     255,204,0
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr10_color.txt
    radius = 0.85r
    color =     153,153,30
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr11_color.txt
    radius = 0.85r
    color =     255,153,0
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr12_color.txt
    radius = 0.85r
    color =     255,204,204
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    <link>
    file = chr13_color.txt
    radius = 0.85r
    color =     102,102,0
    bezier_radius_purity = 0.2
            thickness=2  ##连线的厚度
            z=20   #层数
    crest = 1
    </link>
    
    
        radius=0.40r
        thickness=1
    
    </links>
    
    show_ticks = yes
    show_tick_labels = yes
    
    <ticks>
    radius = 1r
    color = black
    thickness = 2p
    multiplier = 1e-6
    
    <tick>
    spacing = 5u
    size = 10p
    </tick>
    
    <tick>
    color = black
    thickness = 4p
    spacing = 5u
    size = 10p
    show_label = yes
    label_size = 10p
    label_offset = 10p
    format = %d
    </tick>
    
    </ticks>
    
    <image>
    dir* = .
    radius* = 500p
    <<include etc/image.conf>>
    </image>
    
    <<include etc/colors_fonts_patterns.conf>>
    <<include etc/housekeeping.conf>>
    
    

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