关于 GraPhlAn 的孤独自学
最近需要用 GraPhlan 来绘制 taxo分类图，稍微研究了一下
一、简介
官网： http://huttenhower.sph.harvard.edu/GraPhlAn
主要有两个脚本：
graphlan_annotate.py：将原始文件和注释文件合并的，作为 graphlan.py 的输入文件进行绘图
graphlan.py：根据输入文件绘图
Options 分为 4 类（详细选项可以见官网）：
Global tree options：树的枝长等选项
Graphical tree options：树上的一些图形选项
Annotation options：对树上物种的注释选项
Ring options：树外环形图的注释选项
二、学习方法的寻找
我们服务器有该软件，所以无需安装。软件会有 examples 目录，入门级可参考 examples/guide 目录。于是我参考了该目录的内容。
guide 目录中：all.sh
1 source /software/graphlan/activate.sh 2 ##原始 3 graphlan.py guide.txt step_0.png --dpi 300 --size 3.5 4 ##加入线条信息 5 graphlan_annotate.py --annot annot_0.txt guide.txt guide_1.xml 6 graphlan.py guide_1.xml step_1.png --dpi 300 --size 3.5 7 ##加入图像信息 8 graphlan_annotate.py --annot annot_1.txt guide_1.xml guide_2.xml 9 graphlan.py guide_2.xml step_2.png --dpi 300 --size 3.5 10 ##加入注释信息 11 graphlan_annotate.py --annot annot_2.txt guide_2.xml guide_3.xml 12 graphlan.py guide_3.xml step_3.png --dpi 300 --size 3.5 13 ##加入外环信息 14 graphlan_annotate.py --annot annot_3.txt guide_3.xml guide_4.xml 15 graphlan.py guide_4.xml step_4.png --dpi 300 --size 3.5 --pad 0.0
三、对于 all.sh 的解读
以上内容得到结果如下图：
1. 第三行
graphlan.py guide.txt step_0.png --dpi 300 --size 3.5
输入文件各分类水平以 "." 为分隔，用该文件进行绘图，得到一张没有任何注释的分类树，见图 a。输入文件为 guide.txt：
Bacillaceae.Anoxybacillus.Aflavithermus
Bacillaceae.Bacillus.Bamyloliquefaciens
Bacillaceae.Bacillus.Banthracis
Bacillaceae.Bacillus.Batrophaeus
Bacillaceae.Bacillus.Bcellulosilyticus
Bacillaceae.Bacillus.Bcereus
Bacillaceae.Bacillus.Bclausii
Bacillaceae.Bacillus.Bcoagulans
Bacillaceae.Bacillus.Bcoahuilensis
Bacillaceae.Bacillus.Bhalodurans
Bacillaceae.Bacillus.Blicheniformis
Bacillaceae.Bacillus.Bmegaterium
Bacillaceae.Bacillus.Bmycoides
Bacillaceae.Bacillus.Bpseudofirmus
Bacillaceae.Bacillus.Bpseudomycoides
Bacillaceae.Bacillus.Bpumilus
Bacillaceae.Bacillus.Bselenitireducens
Bacillaceae.Bacillus.Bsubtilis
Bacillaceae.Bacillus.Bthuringiensis
Bacillaceae.Bacillus.Bweihenstephanensis
Bacillaceae.Caldalkalibacillus.Cthermarum
Bacillaceae.Geobacillus.Gkaustophilus
Bacillaceae.Geobacillus.Gthermodenitrificans
Bacillaceae.Geobacillus.Gthermoglucosidasius
Bacillaceae.Lysinibacillus.Lfusiformis
Bacillaceae.Lysinibacillus.Lsphaericus
Bacillaceae.Oceanobacillus.Oiheyensis
Listeriaceae.Listeria.Lgrayi
Listeriaceae.Listeria.Linnocua
Listeriaceae.Listeria.Lmonocytogenes
Listeriaceae.Listeria.Lseeligeri
Listeriaceae.Listeria.Lwelshimeri
Paenibacillaceae.Brevibacillus.Bbrevis
Paenibacillaceae.Brevibacillus.Blaterosporus
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus
Paenibacillaceae.Paenibacillus.Plarvae
Paenibacillaceae.Paenibacillus.Pmucilaginosus
Paenibacillaceae.Paenibacillus.Ppolymyxa
Paenibacillaceae.Paenibacillus.Pvortex
Staphylococcaceae.Macrococcus.Mcaseolyticus
Staphylococcaceae.Staphylococcus.Saureus
Staphylococcaceae.Staphylococcus.Scapitis
Staphylococcaceae.Staphylococcus.Scaprae
Staphylococcaceae.Staphylococcus.Scarnosus
Staphylococcaceae.Staphylococcus.Sepidermidis
Staphylococcaceae.Staphylococcus.Shaemolyticus
Staphylococcaceae.Staphylococcus.Shominis
Staphylococcaceae.Staphylococcus.Slugdunensis
Staphylococcaceae.Staphylococcus.Spseudintermedius
Staphylococcaceae.Staphylococcus.Ssaprophyticus
Staphylococcaceae.Staphylococcus.Swarneri
2. 第五、六行
graphlan_annotate.py --annot annot_0.txt guide.txt guide_1.xml graphlan.py guide_1.xml step_1.png --dpi 300 --size 3.5
在原始输入文件的基础上，加入 annot_0.txt ，然后进行绘图，得到了树图的注释，见图 b。该文件使用了 Global tree options，来设置树图的枝长、粗细等。
clade_separation 0.5 branch_thickness 1.5 branch_bracket_depth 0.8 branch_bracket_width 0.25 clade_marker_size 80 clade_marker_edge_color #555555 clade_marker_edge_width 1.2
3. 第八、九行
graphlan_annotate.py --annot annot_1.txt guide_1.xml guide_2.xml graphlan.py guide_2.xml step_2.png --dpi 300 --size 3.5
在以上的基础上，加入 annot_1.txt，然后进行绘图，得到图 c。该文件使用了 Graphical tree options，来设置树图中，枝的颜色、点的图形颜色等。
Proteobacteria clade_marker_color b Proteobacteria clade_marker_size 80 Candidatus_Moranbacteria clade_marker_color r Candidatus_Moranbacteria clade_marker_size 125 Acidobacteria clade_marker_color b Acidobacteria clade_marker_size 120 Acidobacteria clade_marker_shape h Chloroflexi clade_marker_color #20DD20 Plarvae clade_marker_color #008000 Pmucilaginosus clade_marker_color #057005 Ppolymyxa clade_marker_color #009020 Pvortex clade_marker_color #00AA00 Bacillaceae clade_marker_shape * Bacillaceae clade_marker_size 130 Bacillaceae clade_marker_color b Bacteria clade_marker_shape * Bacteria clade_marker_size 130 Paenibacillaceae clade_marker_shape * Paenibacillaceae clade_marker_size 130 Paenibacillaceae clade_marker_color g Staphylococcaceae clade_marker_shape * Staphylococcaceae clade_marker_size 130 Staphylococcaceae clade_marker_color r Batrophaeus clade_marker_size 12 Bcellulosilyticus clade_marker_size 8 Bcereus clade_marker_size 3 Scarnosus clade_marker_size 75 Plarvae clade_marker_size 89 Bpumilus clade_marker_size 50 Bsubtilis clade_marker_size 65 Bthuringiensis clade_marker_size 10 Cthermarum clade_marker_size 15 Bmegaterium clade_marker_size 12 Lfusiformis clade_marker_size 174 Oiheyensis clade_marker_size 95 Scapitis clade_marker_size 36 Shaemolyticus clade_marker_size 64 Ppolymyxa clade_marker_size 20 Pvortex clade_marker_size 19 Swarneri clade_marker_size 33 Spseudintermedius clade_marker_size 19
4. 第十一、十二行
graphlan_annotate.py --annot annot_2.txt guide_2.xml guide_3.xml graphlan.py guide_3.xml step_3.png --dpi 300 --size 3.5
在以上的基础上，加入 annot_2.txt，然后进行绘图，得到图 d。该文件使用了 Annotation options，来设置树图的注释信息。
Proteobacteria clade_marker_color b Proteobacteria clade_marker_size 80 Candidatus_Moranbacteria clade_marker_color r Candidatus_Moranbacteria clade_marker_size 125 Acidobacteria clade_marker_color b Acidobacteria clade_marker_size 120 Acidobacteria clade_marker_shape h Chloroflexi clade_marker_color #20DD20 Plarvae clade_marker_color #008000 Pmucilaginosus clade_marker_color #057005 Ppolymyxa clade_marker_color #009020 Pvortex clade_marker_color #00AA00 Bacillaceae clade_marker_shape * Bacillaceae clade_marker_size 130 Bacillaceae clade_marker_color b Bacteria clade_marker_shape * Bacteria clade_marker_size 130 Paenibacillaceae clade_marker_shape * Paenibacillaceae clade_marker_size 130 Paenibacillaceae clade_marker_color g Staphylococcaceae clade_marker_shape * Staphylococcaceae clade_marker_size 130 Staphylococcaceae clade_marker_color r Batrophaeus clade_marker_size 12 Bcellulosilyticus clade_marker_size 8 Bcereus clade_marker_size 3 Scarnosus clade_marker_size 75 Plarvae clade_marker_size 89 Bpumilus clade_marker_size 50 Bsubtilis clade_marker_size 65 Bthuringiensis clade_marker_size 10 Cthermarum clade_marker_size 15 Bmegaterium clade_marker_size 12 Lfusiformis clade_marker_size 174 Oiheyensis clade_marker_size 95 Scapitis clade_marker_size 36 Shaemolyticus clade_marker_size 64 Ppolymyxa clade_marker_size 20 Pvortex clade_marker_size 19 Swarneri clade_marker_size 33 Spseudintermedius clade_marker_size 19
5. 第十四、十五行
graphlan_annotate.py --annot annot_3.txt guide_3.xml guide_4.xml graphlan.py guide_4.xml step_4.png --dpi 300 --size 3.5 --pad 0.0
在以上的技术上，加入 annot_3.txt，然后进行绘图，得到图 e。该文件使用了 Ring options，来绘制树外的环形图。
ring_internal_separator_thickness 1 0.5 ring_internal_separator_thickness 2 1.0 ring_internal_separator_thickness 3 0.5 ring_internal_separator_thickness 4 0.5 ring_internal_separator_thickness 5 1.0 ring_width 1 0.5 ring_height 1 0.75 ring_width 5 0.5 Bacillaceae.Anoxybacillus.Aflavithermus ring_shape 1 v Bacillaceae.Bacillus.Bamyloliquefaciens ring_shape 1 v Bacillaceae.Bacillus.Banthracis ring_shape 1 ^ Bacillaceae.Bacillus.Batrophaeus ring_shape 1 v Bacillaceae.Bacillus.Bcellulosilyticus ring_shape 1 ^ Bacillaceae.Bacillus.Bcereus ring_shape 1 ^ Bacillaceae.Bacillus.Bclausii ring_shape 1 ^ Bacillaceae.Bacillus.Bcoagulans ring_shape 1 v Bacillaceae.Bacillus.Bcoahuilensis ring_shape 1 ^ Bacillaceae.Bacillus.Bhalodurans ring_shape 1 v Bacillaceae.Bacillus.Blicheniformis ring_shape 1 ^ Bacillaceae.Bacillus.Bmegaterium ring_shape 1 v Bacillaceae.Bacillus.Bmycoides ring_shape 1 v Bacillaceae.Bacillus.Bpseudofirmus ring_shape 1 ^ Bacillaceae.Bacillus.Bpseudomycoides ring_shape 1 v Bacillaceae.Bacillus.Bpumilus ring_shape 1 v Bacillaceae.Bacillus.Bselenitireducens ring_shape 1 ^ Bacillaceae.Bacillus.Bsubtilis ring_shape 1 v Bacillaceae.Bacillus.Bthuringiensis ring_shape 1 ^ Bacillaceae.Bacillus.Bweihenstephanensis ring_shape 1 ^ Bacillaceae.Caldalkalibacillus.Cthermarum ring_shape 1 ^ Bacillaceae.Geobacillus.Gkaustophilus ring_shape 1 v Bacillaceae.Geobacillus.Gthermodenitrificans ring_shape 1 ^ Bacillaceae.Geobacillus.Gthermoglucosidasius ring_shape 1 v Bacillaceae.Lysinibacillus.Lfusiformis ring_shape 1 v Bacillaceae.Lysinibacillus.Lsphaericus ring_shape 1 ^ Bacillaceae.Oceanobacillus.Oiheyensis ring_shape 1 v Listeriaceae.Listeria.Lgrayi ring_shape 1 v Listeriaceae.Listeria.Linnocua ring_shape 1 ^ Listeriaceae.Listeria.Lmonocytogenes ring_shape 1 ^ Listeriaceae.Listeria.Lseeligeri ring_shape 1 v Listeriaceae.Listeria.Lwelshimeri ring_shape 1 ^ Paenibacillaceae.Brevibacillus.Bbrevis ring_shape 1 v Paenibacillaceae.Brevibacillus.Blaterosporus ring_shape 1 ^ Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_shape 1 v Paenibacillaceae.Paenibacillus.Plarvae ring_shape 1 v Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_shape 1 v Paenibacillaceae.Paenibacillus.Ppolymyxa ring_shape 1 v Paenibacillaceae.Paenibacillus.Pvortex ring_shape 1 ^ Staphylococcaceae.Macrococcus.Mcaseolyticus ring_shape 1 ^ Staphylococcaceae.Staphylococcus.Saureus ring_shape 1 ^ Staphylococcaceae.Staphylococcus.Scapitis ring_shape 1 ^ Staphylococcaceae.Staphylococcus.Scaprae ring_shape 1 v Staphylococcaceae.Staphylococcus.Scarnosus ring_shape 1 v Staphylococcaceae.Staphylococcus.Sepidermidis ring_shape 1 v Staphylococcaceae.Staphylococcus.Shaemolyticus ring_shape 1 ^ Staphylococcaceae.Staphylococcus.Shominis ring_shape 1 ^ Staphylococcaceae.Staphylococcus.Slugdunensis ring_shape 1 v Staphylococcaceae.Staphylococcus.Spseudintermedius ring_shape 1 ^ Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_shape 1 v Staphylococcaceae.Staphylococcus.Swarneri ring_shape 1 ^ Bacillaceae.Anoxybacillus.Aflavithermus ring_alpha 2 0.423462136478 Bacillaceae.Bacillus.Bamyloliquefaciens ring_alpha 2 0.328914114867 Bacillaceae.Bacillus.Banthracis ring_alpha 2 0.699584495953 Bacillaceae.Bacillus.Batrophaeus ring_alpha 2 0.914291471541 Bacillaceae.Bacillus.Bcellulosilyticus ring_alpha 2 0.777833777684 Bacillaceae.Bacillus.Bcereus ring_alpha 2 0.594773291359 Bacillaceae.Bacillus.Bclausii ring_alpha 2 0.444201154337 Bacillaceae.Bacillus.Bcoagulans ring_alpha 2 0.85140222384 Bacillaceae.Bacillus.Bcoahuilensis ring_alpha 2 0.445070000889 Bacillaceae.Bacillus.Bhalodurans ring_alpha 2 0.436455399115 Bacillaceae.Bacillus.Blicheniformis ring_alpha 2 0.570138625829 Bacillaceae.Bacillus.Bmegaterium ring_alpha 2 0.331044708077 Bacillaceae.Bacillus.Bmycoides ring_alpha 2 0.134087953967 Bacillaceae.Bacillus.Bpseudofirmus ring_alpha 2 0.959809786409 Bacillaceae.Bacillus.Bpseudomycoides ring_alpha 2 0.322425841569 Bacillaceae.Bacillus.Bpumilus ring_alpha 2 0.6310797781 Bacillaceae.Bacillus.Bselenitireducens ring_alpha 2 0.0999247790029 Bacillaceae.Bacillus.Bsubtilis ring_alpha 2 0.0291140916975 Bacillaceae.Bacillus.Bthuringiensis ring_alpha 2 0.291201092034 Bacillaceae.Bacillus.Bweihenstephanensis ring_alpha 2 0.298583691605 Bacillaceae.Caldalkalibacillus.Cthermarum ring_alpha 2 0.0534558636274 Bacillaceae.Geobacillus.Gkaustophilus ring_alpha 2 0.0878700889869 Bacillaceae.Geobacillus.Gthermodenitrificans ring_alpha 2 0.914114387261 Bacillaceae.Geobacillus.Gthermoglucosidasius ring_alpha 2 0.161880353101 Bacillaceae.Lysinibacillus.Lfusiformis ring_alpha 2 0.730306130149 Bacillaceae.Lysinibacillus.Lsphaericus ring_alpha 2 0.334890327634 Bacillaceae.Oceanobacillus.Oiheyensis ring_alpha 2 0.218075337012 Listeriaceae.Listeria.Lgrayi ring_alpha 2 0.447942203556 Listeriaceae.Listeria.Linnocua ring_alpha 2 0.143522097769 Listeriaceae.Listeria.Lmonocytogenes ring_alpha 2 0.324901346814 Listeriaceae.Listeria.Lseeligeri ring_alpha 2 0.721461557745 Listeriaceae.Listeria.Lwelshimeri ring_alpha 2 0.603871257827 Paenibacillaceae.Brevibacillus.Bbrevis ring_alpha 2 0.536829482998 Paenibacillaceae.Brevibacillus.Blaterosporus ring_alpha 2 0.75932144025 Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_alpha 2 0.904283082241 Paenibacillaceae.Paenibacillus.Plarvae ring_alpha 2 0.253696705619 Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_alpha 2 0.820910759872 Paenibacillaceae.Paenibacillus.Ppolymyxa ring_alpha 2 0.783643352935 Paenibacillaceae.Paenibacillus.Pvortex ring_alpha 2 0.781101978268 Staphylococcaceae.Macrococcus.Mcaseolyticus ring_alpha 2 0.597634927522 Staphylococcaceae.Staphylococcus.Saureus ring_alpha 2 0.639595480173 Staphylococcaceae.Staphylococcus.Scapitis ring_alpha 2 0.326481586152 Staphylococcaceae.Staphylococcus.Scaprae ring_alpha 2 0.48661102115 Staphylococcaceae.Staphylococcus.Scarnosus ring_alpha 2 0.757163548806 Staphylococcaceae.Staphylococcus.Sepidermidis ring_alpha 2 0.899268566505 Staphylococcaceae.Staphylococcus.Shaemolyticus ring_alpha 2 0.895335711479 Staphylococcaceae.Staphylococcus.Shominis ring_alpha 2 0.272427614396 Staphylococcaceae.Staphylococcus.Slugdunensis ring_alpha 2 0.710528488721 Staphylococcaceae.Staphylococcus.Spseudintermedius ring_alpha 2 0.24185085998 Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_alpha 2 0.0895481129751 Staphylococcaceae.Staphylococcus.Swarneri ring_alpha 2 0.00539683704551 Bacillaceae.Anoxybacillus.Aflavithermus ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bamyloliquefaciens ring_color 2 #AAAA00 Bacillaceae.Bacillus.Banthracis ring_color 2 #AAAA00 Bacillaceae.Bacillus.Batrophaeus ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bcellulosilyticus ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bcereus ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bclausii ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bcoagulans ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bcoahuilensis ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bhalodurans ring_color 2 #AAAA00 Bacillaceae.Bacillus.Blicheniformis ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bmegaterium ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bmycoides ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bpseudofirmus ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bpseudomycoides ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bpumilus ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bselenitireducens ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bsubtilis ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bthuringiensis ring_color 2 #AAAA00 Bacillaceae.Bacillus.Bweihenstephanensis ring_color 2 #AAAA00 Bacillaceae.Caldalkalibacillus.Cthermarum ring_color 2 #AAAA00 Bacillaceae.Geobacillus.Gkaustophilus ring_color 2 #AAAA00 Bacillaceae.Geobacillus.Gthermodenitrificans ring_color 2 #AAAA00 Bacillaceae.Geobacillus.Gthermoglucosidasius ring_color 2 #AAAA00 Bacillaceae.Lysinibacillus.Lfusiformis ring_color 2 #AAAA00 Bacillaceae.Lysinibacillus.Lsphaericus ring_color 2 #AAAA00 Bacillaceae.Oceanobacillus.Oiheyensis ring_color 2 #AAAA00 Listeriaceae.Listeria.Lgrayi ring_color 2 #AAAA00 Listeriaceae.Listeria.Linnocua ring_color 2 #AAAA00 Listeriaceae.Listeria.Lmonocytogenes ring_color 2 #AAAA00 Listeriaceae.Listeria.Lseeligeri ring_color 2 #AAAA00 Listeriaceae.Listeria.Lwelshimeri ring_color 2 #AAAA00 Paenibacillaceae.Brevibacillus.Bbrevis ring_color 2 #AAAA00 Paenibacillaceae.Brevibacillus.Blaterosporus ring_color 2 #AAAA00 Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_color 2 #AAAA00 Paenibacillaceae.Paenibacillus.Plarvae ring_color 2 #AAAA00 Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_color 2 #AAAA00 Paenibacillaceae.Paenibacillus.Ppolymyxa ring_color 2 #AAAA00 Paenibacillaceae.Paenibacillus.Pvortex ring_color 2 #AAAA00 Staphylococcaceae.Macrococcus.Mcaseolyticus ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Saureus ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Scapitis ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Scaprae ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Scarnosus ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Sepidermidis ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Shaemolyticus ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Shominis ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Slugdunensis ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Spseudintermedius ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_color 2 #AAAA00 Staphylococcaceae.Staphylococcus.Swarneri ring_color 2 #AAAA00 Bacillaceae.Anoxybacillus.Aflavithermus ring_alpha 3 0.486328798075 Bacillaceae.Bacillus.Bamyloliquefaciens ring_alpha 3 0.902536860011 Bacillaceae.Bacillus.Banthracis ring_alpha 3 0.540967223446 Bacillaceae.Bacillus.Batrophaeus ring_alpha 3 0.514745187899 Bacillaceae.Bacillus.Bcellulosilyticus ring_alpha 3 0.808744341053 Bacillaceae.Bacillus.Bcereus ring_alpha 3 0.174551783411 Bacillaceae.Bacillus.Bclausii ring_alpha 3 0.355096857237 Bacillaceae.Bacillus.Bcoagulans ring_alpha 3 0.30812498305 Bacillaceae.Bacillus.Bcoahuilensis ring_alpha 3 0.899878301907 Bacillaceae.Bacillus.Bhalodurans ring_alpha 3 0.135096627341 Bacillaceae.Bacillus.Blicheniformis ring_alpha 3 0.114946401925 Bacillaceae.Bacillus.Bmegaterium ring_alpha 3 0.112857448 Bacillaceae.Bacillus.Bmycoides ring_alpha 3 0.216895687759 Bacillaceae.Bacillus.Bpseudofirmus ring_alpha 3 0.728546119267 Bacillaceae.Bacillus.Bpseudomycoides ring_alpha 3 0.862047963812 Bacillaceae.Bacillus.Bpumilus ring_alpha 3 0.285139149368 Bacillaceae.Bacillus.Bselenitireducens ring_alpha 3 0.809501074306 Bacillaceae.Bacillus.Bsubtilis ring_alpha 3 0.261975858288 Bacillaceae.Bacillus.Bthuringiensis ring_alpha 3 0.887622203873 Bacillaceae.Bacillus.Bweihenstephanensis ring_alpha 3 0.964470847643 Bacillaceae.Caldalkalibacillus.Cthermarum ring_alpha 3 0.00503110917306 Bacillaceae.Geobacillus.Gkaustophilus ring_alpha 3 0.255498806201 Bacillaceae.Geobacillus.Gthermodenitrificans ring_alpha 3 0.617424889313 Bacillaceae.Geobacillus.Gthermoglucosidasius ring_alpha 3 0.378606726256 Bacillaceae.Lysinibacillus.Lfusiformis ring_alpha 3 0.997919879844 Bacillaceae.Lysinibacillus.Lsphaericus ring_alpha 3 0.707008809187 Bacillaceae.Oceanobacillus.Oiheyensis ring_alpha 3 0.479214513601 Listeriaceae.Listeria.Lgrayi ring_alpha 3 0.204916577728 Listeriaceae.Listeria.Linnocua ring_alpha 3 0.622910173385 Listeriaceae.Listeria.Lmonocytogenes ring_alpha 3 0.952569768174 Listeriaceae.Listeria.Lseeligeri ring_alpha 3 0.354875635794 Listeriaceae.Listeria.Lwelshimeri ring_alpha 3 0.692837888937 Paenibacillaceae.Brevibacillus.Bbrevis ring_alpha 3 0.580492537793 Paenibacillaceae.Brevibacillus.Blaterosporus ring_alpha 3 0.67891660613 Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_alpha 3 0.0180110682393 Paenibacillaceae.Paenibacillus.Plarvae ring_alpha 3 0.953608677163 Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_alpha 3 0.358675673023 Paenibacillaceae.Paenibacillus.Ppolymyxa ring_alpha 3 0.486438688396 Paenibacillaceae.Paenibacillus.Pvortex ring_alpha 3 0.186068756014 Staphylococcaceae.Macrococcus.Mcaseolyticus ring_alpha 3 0.725693055143 Staphylococcaceae.Staphylococcus.Saureus ring_alpha 3 0.374342186447 Staphylococcaceae.Staphylococcus.Scapitis ring_alpha 3 0.510175055083 Staphylococcaceae.Staphylococcus.Scaprae ring_alpha 3 0.948314742048 Staphylococcaceae.Staphylococcus.Scarnosus ring_alpha 3 0.935701022727 Staphylococcaceae.Staphylococcus.Sepidermidis ring_alpha 3 0.0938645581046 Staphylococcaceae.Staphylococcus.Shaemolyticus ring_alpha 3 0.728085338534 Staphylococcaceae.Staphylococcus.Shominis ring_alpha 3 0.741611869641 Staphylococcaceae.Staphylococcus.Slugdunensis ring_alpha 3 0.969166259753 Staphylococcaceae.Staphylococcus.Spseudintermedius ring_alpha 3 0.437648811318 Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_alpha 3 0.781992078475 Staphylococcaceae.Staphylococcus.Swarneri ring_alpha 3 0.867129362962 Bacillaceae.Anoxybacillus.Aflavithermus ring_color 3 #AA00AA Bacillaceae.Bacillus.Bamyloliquefaciens ring_color 3 #AA00AA Bacillaceae.Bacillus.Banthracis ring_color 3 #AA00AA Bacillaceae.Bacillus.Batrophaeus ring_color 3 #AA00AA Bacillaceae.Bacillus.Bcellulosilyticus ring_color 3 #AA00AA Bacillaceae.Bacillus.Bcereus ring_color 3 #AA00AA Bacillaceae.Bacillus.Bclausii ring_color 3 #AA00AA Bacillaceae.Bacillus.Bcoagulans ring_color 3 #AA00AA Bacillaceae.Bacillus.Bcoahuilensis ring_color 3 #AA00AA Bacillaceae.Bacillus.Bhalodurans ring_color 3 #AA00AA Bacillaceae.Bacillus.Blicheniformis ring_color 3 #AA00AA Bacillaceae.Bacillus.Bmegaterium ring_color 3 #AA00AA Bacillaceae.Bacillus.Bmycoides ring_color 3 #AA00AA Bacillaceae.Bacillus.Bpseudofirmus ring_color 3 #AA00AA Bacillaceae.Bacillus.Bpseudomycoides ring_color 3 #AA00AA Bacillaceae.Bacillus.Bpumilus ring_color 3 #AA00AA Bacillaceae.Bacillus.Bselenitireducens ring_color 3 #AA00AA Bacillaceae.Bacillus.Bsubtilis ring_color 3 #AA00AA Bacillaceae.Bacillus.Bthuringiensis ring_color 3 #AA00AA Bacillaceae.Bacillus.Bweihenstephanensis ring_color 3 #AA00AA Bacillaceae.Caldalkalibacillus.Cthermarum ring_color 3 #AA00AA Bacillaceae.Geobacillus.Gkaustophilus ring_color 3 #AA00AA Bacillaceae.Geobacillus.Gthermodenitrificans ring_color 3 #AA00AA Bacillaceae.Geobacillus.Gthermoglucosidasius ring_color 3 #AA00AA Bacillaceae.Lysinibacillus.Lfusiformis ring_color 3 #AA00AA Bacillaceae.Lysinibacillus.Lsphaericus ring_color 3 #AA00AA Bacillaceae.Oceanobacillus.Oiheyensis ring_color 3 #AA00AA Listeriaceae.Listeria.Lgrayi ring_color 3 #AA00AA Listeriaceae.Listeria.Linnocua ring_color 3 #AA00AA Listeriaceae.Listeria.Lmonocytogenes ring_color 3 #AA00AA Listeriaceae.Listeria.Lseeligeri ring_color 3 #AA00AA Listeriaceae.Listeria.Lwelshimeri ring_color 3 #AA00AA Paenibacillaceae.Brevibacillus.Bbrevis ring_color 3 #AA00AA Paenibacillaceae.Brevibacillus.Blaterosporus ring_color 3 #AA00AA Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_color 3 #AA00AA Paenibacillaceae.Paenibacillus.Plarvae ring_color 3 #AA00AA Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_color 3 #AA00AA Paenibacillaceae.Paenibacillus.Ppolymyxa ring_color 3 #AA00AA Paenibacillaceae.Paenibacillus.Pvortex ring_color 3 #AA00AA Staphylococcaceae.Macrococcus.Mcaseolyticus ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Saureus ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Scapitis ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Scaprae ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Scarnosus ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Sepidermidis ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Shaemolyticus ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Shominis ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Slugdunensis ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Spseudintermedius ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_color 3 #AA00AA Staphylococcaceae.Staphylococcus.Swarneri ring_color 3 #AA00AA Bacillaceae.Anoxybacillus.Aflavithermus ring_alpha 4 0.0164337819514 Bacillaceae.Bacillus.Bamyloliquefaciens ring_alpha 4 0.961779754562 Bacillaceae.Bacillus.Banthracis ring_alpha 4 0.0911294036676 Bacillaceae.Bacillus.Batrophaeus ring_alpha 4 0.214683813052 Bacillaceae.Bacillus.Bcellulosilyticus ring_alpha 4 0.1835464929 Bacillaceae.Bacillus.Bcereus ring_alpha 4 0.649839771735 Bacillaceae.Bacillus.Bclausii ring_alpha 4 0.508572486958 Bacillaceae.Bacillus.Bcoagulans ring_alpha 4 0.54485221387 Bacillaceae.Bacillus.Bcoahuilensis ring_alpha 4 0.011849863671 Bacillaceae.Bacillus.Bhalodurans ring_alpha 4 0.494163373827 Bacillaceae.Bacillus.Blicheniformis ring_alpha 4 0.0037027183784 Bacillaceae.Bacillus.Bmegaterium ring_alpha 4 0.944619736609 Bacillaceae.Bacillus.Bmycoides ring_alpha 4 0.740793384052 Bacillaceae.Bacillus.Bpseudofirmus ring_alpha 4 0.679054870785 Bacillaceae.Bacillus.Bpseudomycoides ring_alpha 4 0.65485119746 Bacillaceae.Bacillus.Bpumilus ring_alpha 4 0.696989248748 Bacillaceae.Bacillus.Bselenitireducens ring_alpha 4 0.250910763296 Bacillaceae.Bacillus.Bsubtilis ring_alpha 4 0.603110791976 Bacillaceae.Bacillus.Bthuringiensis ring_alpha 4 0.768995251147 Bacillaceae.Bacillus.Bweihenstephanensis ring_alpha 4 0.382492089443 Bacillaceae.Caldalkalibacillus.Cthermarum ring_alpha 4 0.202515841523 Bacillaceae.Geobacillus.Gkaustophilus ring_alpha 4 0.604966298977 Bacillaceae.Geobacillus.Gthermodenitrificans ring_alpha 4 0.271415944271 Bacillaceae.Geobacillus.Gthermoglucosidasius ring_alpha 4 0.729366061868 Bacillaceae.Lysinibacillus.Lfusiformis ring_alpha 4 0.281874921267 Bacillaceae.Lysinibacillus.Lsphaericus ring_alpha 4 0.986149233417 Bacillaceae.Oceanobacillus.Oiheyensis ring_alpha 4 0.0868426043474 Listeriaceae.Listeria.Lgrayi ring_alpha 4 0.581618564755 Listeriaceae.Listeria.Linnocua ring_alpha 4 0.587717564353 Listeriaceae.Listeria.Lmonocytogenes ring_alpha 4 0.520464993313 Listeriaceae.Listeria.Lseeligeri ring_alpha 4 0.689907782867 Listeriaceae.Listeria.Lwelshimeri ring_alpha 4 0.432283970377 Paenibacillaceae.Brevibacillus.Bbrevis ring_alpha 4 0.713859589198 Paenibacillaceae.Brevibacillus.Blaterosporus ring_alpha 4 0.91882698904 Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_alpha 4 0.0448745597998 Paenibacillaceae.Paenibacillus.Plarvae ring_alpha 4 0.702703981052 Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_alpha 4 0.365023286887 Paenibacillaceae.Paenibacillus.Ppolymyxa ring_alpha 4 0.73860888919 Paenibacillaceae.Paenibacillus.Pvortex ring_alpha 4 0.905904555893 Staphylococcaceae.Macrococcus.Mcaseolyticus ring_alpha 4 0.252754272893 Staphylococcaceae.Staphylococcus.Saureus ring_alpha 4 0.483919418674 Staphylococcaceae.Staphylococcus.Scapitis ring_alpha 4 0.652801998863 Staphylococcaceae.Staphylococcus.Scaprae ring_alpha 4 0.726258452089 Staphylococcaceae.Staphylococcus.Scarnosus ring_alpha 4 0.833070576852 Staphylococcaceae.Staphylococcus.Sepidermidis ring_alpha 4 0.645235993575 Staphylococcaceae.Staphylococcus.Shaemolyticus ring_alpha 4 0.470807178843 Staphylococcaceae.Staphylococcus.Shominis ring_alpha 4 0.777865349824 Staphylococcaceae.Staphylococcus.Slugdunensis ring_alpha 4 0.00619809441301 Staphylococcaceae.Staphylococcus.Spseudintermedius ring_alpha 4 0.652324807659 Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_alpha 4 0.580610729368 Staphylococcaceae.Staphylococcus.Swarneri ring_alpha 4 0.243468671906 Bacillaceae.Anoxybacillus.Aflavithermus ring_color 4 #00AAAA Bacillaceae.Bacillus.Bamyloliquefaciens ring_color 4 #00AAAA Bacillaceae.Bacillus.Banthracis ring_color 4 #00AAAA Bacillaceae.Bacillus.Batrophaeus ring_color 4 #00AAAA Bacillaceae.Bacillus.Bcellulosilyticus ring_color 4 #00AAAA Bacillaceae.Bacillus.Bcereus ring_color 4 #00AAAA Bacillaceae.Bacillus.Bclausii ring_color 4 #00AAAA Bacillaceae.Bacillus.Bcoagulans ring_color 4 #00AAAA Bacillaceae.Bacillus.Bcoahuilensis ring_color 4 #00AAAA Bacillaceae.Bacillus.Bhalodurans ring_color 4 #00AAAA Bacillaceae.Bacillus.Blicheniformis ring_color 4 #00AAAA Bacillaceae.Bacillus.Bmegaterium ring_color 4 #00AAAA Bacillaceae.Bacillus.Bmycoides ring_color 4 #00AAAA Bacillaceae.Bacillus.Bpseudofirmus ring_color 4 #00AAAA Bacillaceae.Bacillus.Bpseudomycoides ring_color 4 #00AAAA Bacillaceae.Bacillus.Bpumilus ring_color 4 #00AAAA Bacillaceae.Bacillus.Bselenitireducens ring_color 4 #00AAAA Bacillaceae.Bacillus.Bsubtilis ring_color 4 #00AAAA Bacillaceae.Bacillus.Bthuringiensis ring_color 4 #00AAAA Bacillaceae.Bacillus.Bweihenstephanensis ring_color 4 #00AAAA Bacillaceae.Caldalkalibacillus.Cthermarum ring_color 4 #00AAAA Bacillaceae.Geobacillus.Gkaustophilus ring_color 4 #00AAAA Bacillaceae.Geobacillus.Gthermodenitrificans ring_color 4 #00AAAA Bacillaceae.Geobacillus.Gthermoglucosidasius ring_color 4 #00AAAA Bacillaceae.Lysinibacillus.Lfusiformis ring_color 4 #00AAAA Bacillaceae.Lysinibacillus.Lsphaericus ring_color 4 #00AAAA Bacillaceae.Oceanobacillus.Oiheyensis ring_color 4 #00AAAA Listeriaceae.Listeria.Lgrayi ring_color 4 #00AAAA Listeriaceae.Listeria.Linnocua ring_color 4 #00AAAA Listeriaceae.Listeria.Lmonocytogenes ring_color 4 #00AAAA Listeriaceae.Listeria.Lseeligeri ring_color 4 #00AAAA Listeriaceae.Listeria.Lwelshimeri ring_color 4 #00AAAA Paenibacillaceae.Brevibacillus.Bbrevis ring_color 4 #00AAAA Paenibacillaceae.Brevibacillus.Blaterosporus ring_color 4 #00AAAA Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_color 4 #00AAAA Paenibacillaceae.Paenibacillus.Plarvae ring_color 4 #00AAAA Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_color 4 #00AAAA Paenibacillaceae.Paenibacillus.Ppolymyxa ring_color 4 #00AAAA Paenibacillaceae.Paenibacillus.Pvortex ring_color 4 #00AAAA Staphylococcaceae.Macrococcus.Mcaseolyticus ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Saureus ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Scapitis ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Scaprae ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Scarnosus ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Sepidermidis ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Shaemolyticus ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Shominis ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Slugdunensis ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Spseudintermedius ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_color 4 #00AAAA Staphylococcaceae.Staphylococcus.Swarneri ring_color 4 #00AAAA Bacillaceae.Anoxybacillus.Aflavithermus ring_height 5 2.48900854747 Bacillaceae.Bacillus.Bamyloliquefaciens ring_height 5 2.5569451352 Bacillaceae.Bacillus.Banthracis ring_height 5 1.4616581923 Bacillaceae.Bacillus.Batrophaeus ring_height 5 1.5214251868 Bacillaceae.Bacillus.Bcellulosilyticus ring_height 5 0.275406475474 Bacillaceae.Bacillus.Bcereus ring_height 5 3.96420929693 Bacillaceae.Bacillus.Bclausii ring_height 5 0.36682224696 Bacillaceae.Bacillus.Bcoagulans ring_height 5 3.11304018594 Bacillaceae.Bacillus.Bcoahuilensis ring_height 5 3.17186920433 Bacillaceae.Bacillus.Bhalodurans ring_height 5 1.03261323231 Bacillaceae.Bacillus.Blicheniformis ring_height 5 2.84479580061 Bacillaceae.Bacillus.Bmegaterium ring_height 5 1.97722308257 Bacillaceae.Bacillus.Bmycoides ring_height 5 2.66122684072 Bacillaceae.Bacillus.Bpseudofirmus ring_height 5 1.43290815777 Bacillaceae.Bacillus.Bpseudomycoides ring_height 5 1.11687288226 Bacillaceae.Bacillus.Bpumilus ring_height 5 1.08510776094 Bacillaceae.Bacillus.Bselenitireducens ring_height 5 2.77859614711 Bacillaceae.Bacillus.Bsubtilis ring_height 5 0.554574632132 Bacillaceae.Bacillus.Bthuringiensis ring_height 5 1.57378483828 Bacillaceae.Bacillus.Bweihenstephanensis ring_height 5 2.70028276238 Bacillaceae.Caldalkalibacillus.Cthermarum ring_height 5 1.86166458022 Bacillaceae.Geobacillus.Gkaustophilus ring_height 5 0.0242900869783 Bacillaceae.Geobacillus.Gthermodenitrificans ring_height 5 3.07841560635 Bacillaceae.Geobacillus.Gthermoglucosidasius ring_height 5 3.46510209264 Bacillaceae.Lysinibacillus.Lfusiformis ring_height 5 1.35283141925 Bacillaceae.Lysinibacillus.Lsphaericus ring_height 5 3.92974800987 Bacillaceae.Oceanobacillus.Oiheyensis ring_height 5 2.28533114154 Listeriaceae.Listeria.Lgrayi ring_height 5 0.818507572602 Listeriaceae.Listeria.Linnocua ring_height 5 0.800083345466 Listeriaceae.Listeria.Lmonocytogenes ring_height 5 0.978937868742 Listeriaceae.Listeria.Lseeligeri ring_height 5 0.892990893608 Listeriaceae.Listeria.Lwelshimeri ring_height 5 2.52510303764 Paenibacillaceae.Brevibacillus.Bbrevis ring_height 5 1.94634642846 Paenibacillaceae.Brevibacillus.Blaterosporus ring_height 5 2.53149220001 Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_height 5 0.617175345723 Paenibacillaceae.Paenibacillus.Plarvae ring_height 5 1.49321243619 Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_height 5 0.0817469468168 Paenibacillaceae.Paenibacillus.Ppolymyxa ring_height 5 3.26055825675 Paenibacillaceae.Paenibacillus.Pvortex ring_height 5 2.50175369758 Staphylococcaceae.Macrococcus.Mcaseolyticus ring_height 5 2.6642090736 Staphylococcaceae.Staphylococcus.Saureus ring_height 5 1.21391731853 Staphylococcaceae.Staphylococcus.Scapitis ring_height 5 0.92038173113 Staphylococcaceae.Staphylococcus.Scaprae ring_height 5 3.22193378354 Staphylococcaceae.Staphylococcus.Scarnosus ring_height 5 2.59751672494 Staphylococcaceae.Staphylococcus.Sepidermidis ring_height 5 0.365700208191 Staphylococcaceae.Staphylococcus.Shaemolyticus ring_height 5 1.34748130999 Staphylococcaceae.Staphylococcus.Shominis ring_height 5 0.0961524114391 Staphylococcaceae.Staphylococcus.Slugdunensis ring_height 5 2.02393979902 Staphylococcaceae.Staphylococcus.Spseudintermedius ring_height 5 1.94654560527 Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_height 5 2.75289926136 Staphylococcaceae.Staphylococcus.Swarneri ring_height 5 2.39465498028 Bacillaceae.Bacillus.Bsubtilis clade_marker_label 65 Staphylococcaceae.Staphylococcus.Saureus clade_marker_label 17 Bacillaceae.Bacillus.Banthracis clade_marker_label x Bacillaceae.Bacillus.Banthracis clade_marker_font_color w Bacillaceae.Bacillus.Banthracis clade_marker_edge_color b Bacillaceae.Lysinibacillus.Lfusiformis clade_marker_label 156 Bacillaceae.Lysinibacillus.Lfusiformis clade_marker_edge_color b Bacillaceae.Oceanobacillus.Oiheyensis clade_marker_label 18 Bacillaceae.Oceanobacillus.Oiheyensis clade_marker_color k Bacillaceae.Oceanobacillus.Oiheyensis clade_marker_font_color w
四、输入文件的处理
经过以上学习，已经大致了解了 GraPhlan 图的构成，以及 options 的内容。但是，一直有一个疑惑盘卧于心：如果数据量小，我可以手动写入注释文件，那如果数据量很大呢？要知道 Meta 注释的结果可能上万呀！经过各种检索，最后终于在 bitbucket 中找到了一个脚本 export2graphlan.py。可以根据物种样本丰度矩阵，来生成对应的 tree.txt 和 annot.txt（tree.txt 即上文中的 guide.txt）
网址：https://bitbucket.org/CibioCM/export2graphlan/src/default/
由于还没仔细研究这个脚本，我就在这里简单的举个例子，以最近分析的一个 Meta 结果为输入文件：（这里我是用的是“管道符”作为分隔符，没有使用“点”，也是可以的。）
ID SRS014459-Stool_profile SRS014464-Anterior_nares_profile SRS014470-Tongue_dorsum_profile SRS014472-Buccal_mucosa_profile #SampleID TKS TMS PTS KTS k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas aeruginosa 0 0 2.218786516 20.10325925 k__Bacteria|p__Candidatus Moranbacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Candidatus Moranbacteria bacterium RBG_13_45_13 0 0 0 7.310276093 k__Bacteria 0 0 0 9.278427348 k__Bacteria|p__Acidobacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified 0 0 0 7.389306104 k__Bacteria|p__Chloroflexi 0 0 0 13.67021629 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfococcus|s__Desulfococcus multivorans 0 0 0 5.960850128 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Actinobacteria bacterium 0 0 0 7.53872222 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Cohaesibacteraceae|g__Cohaesibacter 0 0 0 11.39184691 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Pseudoruegeria|s__Pseudoruegeria lutimaris 0 0 0 7.16969386 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Unclassified|s__Desulfobacteraceae bacterium 0 0 0 14.23980864 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_70_13 0 0 0 13.14443874 k__Bacteria|p__Chloroflexi|c__Anaerolineae 0 13.68106333 2.112284763 8.202129776 k__Bacteria|p__Acidobacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Acidobacteria bacterium 0 0 0 29.01696855 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli 0 0 0 12.84794764 k__Bacteria|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__bacterium HR39 0.724322421 0 0 10.29383757 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae 0 0 0 5.759922595 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 0 0 0 14.54278329 k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Ignavibacteria bacterium RBG_13_36_8 0 0 0 10.05162963 k__Unclassified|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__uncultured prokaryote 0 0 0 9.685375916 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium 0 0 0 10.88393017 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__SAR86 cluster bacterium 0 0 0 8.946476632 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Unclassified|g__Methyloceanibacter|s__Methyloceanibacter marginalis 0 0 0 9.764440209 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Cellulomonadaceae 1.748909409 0 3.840517751 16.15571016 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales 0 0 0 12.65760768 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Syntrophobacterales|f__Unclassified|g__Unclassified|s__Syntrophobacterales bacterium RBG_19FT_COMBO_59_10 0 0 0 12.89643047 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides 0 0 0 13.22924157 k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Ilumatobacteraceae 0 0 0 8.175966682 k__Bacteria|p__Actinobacteria|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter|s__Patulibacter minatonensis 0 0 0 8.41762087 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium 0 0 0 12.2853251 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_52_11 0 0 0 11.90192961 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae 0 0 0 9.526283131 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter 0 0 0 8.543885183 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter|s__Lysobacter maris 1.466311242 0 0 8.33549774 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptosporangiales|f__Thermomonosporaceae|g__Thermomonospora|s__Thermomonospora curvata 0 0 0 34.67083842 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptosporangiales|f__Streptosporangiaceae|g__Thermoactinospora|s__Thermoactinospora rubra 0 0 0 20.59686607 k__Bacteria|p__Acidobacteria|c__Solibacteres|o__Solibacterales|f__Solibacteraceae|g__Candidatus Solibacter|s__Candidatus Solibacter usitatus 0 0 0 25.93679431 k__Bacteria|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__bacterium 0 0 2.490901843 4.836161424 k__Bacteria|p__Acidobacteria|c__Solibacteres|o__Solibacterales|f__Solibacteraceae|g__Candidatus Sulfopaludibacter|s__Candidatus Sulfopaludibacter sp. SbA3 0 0 0 21.90739791 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_69_14 0.81516964 2.318824293 0 8.109450343 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium CSP1-4 0 0 0 8.67399511 k__Bacteria|p__Proteobacteria|c__Candidatus Muproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Candidatus Muproteobacteria bacterium RIFCSPLOWO2_01_FULL_60_18 0 0 0 5.817113316 k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus Nitrosocosmicus|s__Candidatus Nitrosocosmicus oleophilus 0 0 1.307106908 16.0726553 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae 0 0 0 16.64711153 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__delta proteobacterium MLMS-1 0 0 0 23.18441205 k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus 0 0 0 21.67229412 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Intrasporangiaceae|g__Phycicoccus 0 0 0 20.59542944 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium 0 0 0 17.37739359 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium HGW-Chloroflexi-8 0 0 0 27.70989789 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Hyphomicrobiaceae|g__Rhodoplanes|s__Rhodoplanes sp. Z2-YC6860 0 0 0 20.55671623 k__Bacteria|p__Proteobacteria|c__Betaproteobacteria 0 0 0 13.80829929 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium HGW-Chloroflexi-6 0 0 0 15.83063195 k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Haloferacaceae|g__Halobellus|s__Halobellus limi 0 0 0 7.901859129 k__Bacteria|p__Chlorobi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chlorobi bacterium OLB5 0.726510706 0 0 11.35743045 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria 0 0 0 33.09793359 k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__uncultured Chloroflexi bacterium 0 0 0 7.594564607 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. U41 0 0 0 9.672322849 k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Unclassified|g__Bauldia|s__Bauldia litoralis 0 0 0 7.811552167 k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea|s__Anaerolinea thermolimosa 0 0 0 5.339928239 k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea|s__Longilinea arvoryzae 0 0 0 12.65760768 k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Algoriphagus 0 0 0 11.61304782 k__Bacteria|p__candidate division NC10|c__Unclassified|o__Unclassified|f__Unclassified|g__Candidatus Methylomirabilis 0 0 0 11.39184691 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora|s__Actinomycetospora cinnamomea 0 0 0 5.960850128 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__marine actinobacterium MedAcidi-G2B 0 0 0 11.94948977 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobacter|s__Desulfobacter curvatus 1.422929253 0 0 24.26665614 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis 1.64708934 0 0 14.04474277 k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Unclassified|g__Unclassified|s__Anaerolineales bacterium 0 4.023842156 3.106301122 6.030977776 k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfatitalea|s__Desulfatitalea sp. BRH_c12 0 0 0 14.44036932 k__Bacteria|p__Actinobacteria 0 0 0 8.993563351 Unclassified 0 0 0 12.52506728 k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified 0 0 0 10.05162963 k__Bacteria|p__Proteobacteria 0 0 0 33.39629388 k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Ignavibacteria bacterium RBG_16_34_14 0 0 0 13.20793845
目前遇到的需要去除的特殊字符：
- 如果使用了其他分隔符，“点”是不可以出现的，否则会导致分割出错
- (class) 也不可以
执行命令 work.sh：
1 source /software/graphlan/activate.sh 2 export2graphlan.py --skip_rows 1,2 -i table.txt --tree tree.txt --annotation annot.txt --most_abundant 40 --abundance_threshold 1 --least_biomarkers 10 --annotations 3,4,5,6 --external_annotations 7 --min_clade_size 1 3 graphlan_annotate.py --annot annot.txt tree.txt abundance.xml 4 graphlan.py --dpi 300 abundance.xml abundance.png --size 12
得到结果：
转载请注明出处：https://www.cnblogs.com/Shinamy/p/10905115.html
