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
source /software/graphlan/activate.sh
##原始
graphlan.py guide.txt step_0.png --dpi --size 3.5
##加入线条信息
graphlan_annotate.py --annot annot_0.txt guide.txt guide_1.xml
graphlan.py guide_1.xml step_1.png --dpi --size 3.5
##加入图像信息
graphlan_annotate.py --annot annot_1.txt guide_1.xml guide_2.xml
graphlan.py guide_2.xml step_2.png --dpi --size 3.5
##加入注释信息
graphlan_annotate.py --annot annot_2.txt guide_2.xml guide_3.xml
graphlan.py guide_3.xml step_3.png --dpi --size 3.5
##加入外环信息
graphlan_annotate.py --annot annot_3.txt guide_3.xml guide_4.xml
graphlan.py guide_4.xml step_4.png --dpi --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
guide.txt
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
clade_marker_edge_color #
clade_marker_edge_width 1.2
annot_0.txt
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
Candidatus_Moranbacteria clade_marker_color r
Candidatus_Moranbacteria clade_marker_size
Acidobacteria clade_marker_color b
Acidobacteria clade_marker_size
Acidobacteria clade_marker_shape h
Chloroflexi clade_marker_color #20DD20
Plarvae clade_marker_color #
Pmucilaginosus clade_marker_color #
Ppolymyxa clade_marker_color #
Pvortex clade_marker_color #00AA00
Bacillaceae clade_marker_shape *
Bacillaceae clade_marker_size
Bacillaceae clade_marker_color b
Bacteria clade_marker_shape *
Bacteria clade_marker_size
Paenibacillaceae clade_marker_shape *
Paenibacillaceae clade_marker_size
Paenibacillaceae clade_marker_color g
Staphylococcaceae clade_marker_shape *
Staphylococcaceae clade_marker_size
Staphylococcaceae clade_marker_color r
Batrophaeus clade_marker_size
Bcellulosilyticus clade_marker_size
Bcereus clade_marker_size
Scarnosus clade_marker_size
Plarvae clade_marker_size
Bpumilus clade_marker_size
Bsubtilis clade_marker_size
Bthuringiensis clade_marker_size
Cthermarum clade_marker_size
Bmegaterium clade_marker_size
Lfusiformis clade_marker_size
Oiheyensis clade_marker_size
Scapitis clade_marker_size
Shaemolyticus clade_marker_size
Ppolymyxa clade_marker_size
Pvortex clade_marker_size
Swarneri clade_marker_size
Spseudintermedius clade_marker_size
annot_1.txt
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
Candidatus_Moranbacteria clade_marker_color r
Candidatus_Moranbacteria clade_marker_size
Acidobacteria clade_marker_color b
Acidobacteria clade_marker_size
Acidobacteria clade_marker_shape h
Chloroflexi clade_marker_color #20DD20
Plarvae clade_marker_color #
Pmucilaginosus clade_marker_color #
Ppolymyxa clade_marker_color #
Pvortex clade_marker_color #00AA00
Bacillaceae clade_marker_shape *
Bacillaceae clade_marker_size
Bacillaceae clade_marker_color b
Bacteria clade_marker_shape *
Bacteria clade_marker_size
Paenibacillaceae clade_marker_shape *
Paenibacillaceae clade_marker_size
Paenibacillaceae clade_marker_color g
Staphylococcaceae clade_marker_shape *
Staphylococcaceae clade_marker_size
Staphylococcaceae clade_marker_color r
Batrophaeus clade_marker_size
Bcellulosilyticus clade_marker_size
Bcereus clade_marker_size
Scarnosus clade_marker_size
Plarvae clade_marker_size
Bpumilus clade_marker_size
Bsubtilis clade_marker_size
Bthuringiensis clade_marker_size
Cthermarum clade_marker_size
Bmegaterium clade_marker_size
Lfusiformis clade_marker_size
Oiheyensis clade_marker_size
Scapitis clade_marker_size
Shaemolyticus clade_marker_size
Ppolymyxa clade_marker_size
Pvortex clade_marker_size
Swarneri clade_marker_size
Spseudintermedius clade_marker_size
annot_2.txt
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 0.5
ring_internal_separator_thickness 1.0
ring_internal_separator_thickness 0.5
ring_internal_separator_thickness 0.5
ring_internal_separator_thickness 1.0
ring_width 0.5
ring_height 0.75
ring_width 0.5
Bacillaceae.Anoxybacillus.Aflavithermus ring_shape v
Bacillaceae.Bacillus.Bamyloliquefaciens ring_shape v
Bacillaceae.Bacillus.Banthracis ring_shape ^
Bacillaceae.Bacillus.Batrophaeus ring_shape v
Bacillaceae.Bacillus.Bcellulosilyticus ring_shape ^
Bacillaceae.Bacillus.Bcereus ring_shape ^
Bacillaceae.Bacillus.Bclausii ring_shape ^
Bacillaceae.Bacillus.Bcoagulans ring_shape v
Bacillaceae.Bacillus.Bcoahuilensis ring_shape ^
Bacillaceae.Bacillus.Bhalodurans ring_shape v
Bacillaceae.Bacillus.Blicheniformis ring_shape ^
Bacillaceae.Bacillus.Bmegaterium ring_shape v
Bacillaceae.Bacillus.Bmycoides ring_shape v
Bacillaceae.Bacillus.Bpseudofirmus ring_shape ^
Bacillaceae.Bacillus.Bpseudomycoides ring_shape v
Bacillaceae.Bacillus.Bpumilus ring_shape v
Bacillaceae.Bacillus.Bselenitireducens ring_shape ^
Bacillaceae.Bacillus.Bsubtilis ring_shape v
Bacillaceae.Bacillus.Bthuringiensis ring_shape ^
Bacillaceae.Bacillus.Bweihenstephanensis ring_shape ^
Bacillaceae.Caldalkalibacillus.Cthermarum ring_shape ^
Bacillaceae.Geobacillus.Gkaustophilus ring_shape v
Bacillaceae.Geobacillus.Gthermodenitrificans ring_shape ^
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_shape v
Bacillaceae.Lysinibacillus.Lfusiformis ring_shape v
Bacillaceae.Lysinibacillus.Lsphaericus ring_shape ^
Bacillaceae.Oceanobacillus.Oiheyensis ring_shape v
Listeriaceae.Listeria.Lgrayi ring_shape v
Listeriaceae.Listeria.Linnocua ring_shape ^
Listeriaceae.Listeria.Lmonocytogenes ring_shape ^
Listeriaceae.Listeria.Lseeligeri ring_shape v
Listeriaceae.Listeria.Lwelshimeri ring_shape ^
Paenibacillaceae.Brevibacillus.Bbrevis ring_shape v
Paenibacillaceae.Brevibacillus.Blaterosporus ring_shape ^
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_shape v
Paenibacillaceae.Paenibacillus.Plarvae ring_shape v
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_shape v
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_shape v
Paenibacillaceae.Paenibacillus.Pvortex ring_shape ^
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_shape ^
Staphylococcaceae.Staphylococcus.Saureus ring_shape ^
Staphylococcaceae.Staphylococcus.Scapitis ring_shape ^
Staphylococcaceae.Staphylococcus.Scaprae ring_shape v
Staphylococcaceae.Staphylococcus.Scarnosus ring_shape v
Staphylococcaceae.Staphylococcus.Sepidermidis ring_shape v
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_shape ^
Staphylococcaceae.Staphylococcus.Shominis ring_shape ^
Staphylococcaceae.Staphylococcus.Slugdunensis ring_shape v
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_shape ^
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_shape v
Staphylococcaceae.Staphylococcus.Swarneri ring_shape ^
Bacillaceae.Anoxybacillus.Aflavithermus ring_alpha 0.423462136478
Bacillaceae.Bacillus.Bamyloliquefaciens ring_alpha 0.328914114867
Bacillaceae.Bacillus.Banthracis ring_alpha 0.699584495953
Bacillaceae.Bacillus.Batrophaeus ring_alpha 0.914291471541
Bacillaceae.Bacillus.Bcellulosilyticus ring_alpha 0.777833777684
Bacillaceae.Bacillus.Bcereus ring_alpha 0.594773291359
Bacillaceae.Bacillus.Bclausii ring_alpha 0.444201154337
Bacillaceae.Bacillus.Bcoagulans ring_alpha 0.85140222384
Bacillaceae.Bacillus.Bcoahuilensis ring_alpha 0.445070000889
Bacillaceae.Bacillus.Bhalodurans ring_alpha 0.436455399115
Bacillaceae.Bacillus.Blicheniformis ring_alpha 0.570138625829
Bacillaceae.Bacillus.Bmegaterium ring_alpha 0.331044708077
Bacillaceae.Bacillus.Bmycoides ring_alpha 0.134087953967
Bacillaceae.Bacillus.Bpseudofirmus ring_alpha 0.959809786409
Bacillaceae.Bacillus.Bpseudomycoides ring_alpha 0.322425841569
Bacillaceae.Bacillus.Bpumilus ring_alpha 0.6310797781
Bacillaceae.Bacillus.Bselenitireducens ring_alpha 0.0999247790029
Bacillaceae.Bacillus.Bsubtilis ring_alpha 0.0291140916975
Bacillaceae.Bacillus.Bthuringiensis ring_alpha 0.291201092034
Bacillaceae.Bacillus.Bweihenstephanensis ring_alpha 0.298583691605
Bacillaceae.Caldalkalibacillus.Cthermarum ring_alpha 0.0534558636274
Bacillaceae.Geobacillus.Gkaustophilus ring_alpha 0.0878700889869
Bacillaceae.Geobacillus.Gthermodenitrificans ring_alpha 0.914114387261
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_alpha 0.161880353101
Bacillaceae.Lysinibacillus.Lfusiformis ring_alpha 0.730306130149
Bacillaceae.Lysinibacillus.Lsphaericus ring_alpha 0.334890327634
Bacillaceae.Oceanobacillus.Oiheyensis ring_alpha 0.218075337012
Listeriaceae.Listeria.Lgrayi ring_alpha 0.447942203556
Listeriaceae.Listeria.Linnocua ring_alpha 0.143522097769
Listeriaceae.Listeria.Lmonocytogenes ring_alpha 0.324901346814
Listeriaceae.Listeria.Lseeligeri ring_alpha 0.721461557745
Listeriaceae.Listeria.Lwelshimeri ring_alpha 0.603871257827
Paenibacillaceae.Brevibacillus.Bbrevis ring_alpha 0.536829482998
Paenibacillaceae.Brevibacillus.Blaterosporus ring_alpha 0.75932144025
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_alpha 0.904283082241
Paenibacillaceae.Paenibacillus.Plarvae ring_alpha 0.253696705619
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_alpha 0.820910759872
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_alpha 0.783643352935
Paenibacillaceae.Paenibacillus.Pvortex ring_alpha 0.781101978268
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_alpha 0.597634927522
Staphylococcaceae.Staphylococcus.Saureus ring_alpha 0.639595480173
Staphylococcaceae.Staphylococcus.Scapitis ring_alpha 0.326481586152
Staphylococcaceae.Staphylococcus.Scaprae ring_alpha 0.48661102115
Staphylococcaceae.Staphylococcus.Scarnosus ring_alpha 0.757163548806
Staphylococcaceae.Staphylococcus.Sepidermidis ring_alpha 0.899268566505
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_alpha 0.895335711479
Staphylococcaceae.Staphylococcus.Shominis ring_alpha 0.272427614396
Staphylococcaceae.Staphylococcus.Slugdunensis ring_alpha 0.710528488721
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_alpha 0.24185085998
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_alpha 0.0895481129751
Staphylococcaceae.Staphylococcus.Swarneri ring_alpha 0.00539683704551
Bacillaceae.Anoxybacillus.Aflavithermus ring_color #AAAA00
Bacillaceae.Bacillus.Bamyloliquefaciens ring_color #AAAA00
Bacillaceae.Bacillus.Banthracis ring_color #AAAA00
Bacillaceae.Bacillus.Batrophaeus ring_color #AAAA00
Bacillaceae.Bacillus.Bcellulosilyticus ring_color #AAAA00
Bacillaceae.Bacillus.Bcereus ring_color #AAAA00
Bacillaceae.Bacillus.Bclausii ring_color #AAAA00
Bacillaceae.Bacillus.Bcoagulans ring_color #AAAA00
Bacillaceae.Bacillus.Bcoahuilensis ring_color #AAAA00
Bacillaceae.Bacillus.Bhalodurans ring_color #AAAA00
Bacillaceae.Bacillus.Blicheniformis ring_color #AAAA00
Bacillaceae.Bacillus.Bmegaterium ring_color #AAAA00
Bacillaceae.Bacillus.Bmycoides ring_color #AAAA00
Bacillaceae.Bacillus.Bpseudofirmus ring_color #AAAA00
Bacillaceae.Bacillus.Bpseudomycoides ring_color #AAAA00
Bacillaceae.Bacillus.Bpumilus ring_color #AAAA00
Bacillaceae.Bacillus.Bselenitireducens ring_color #AAAA00
Bacillaceae.Bacillus.Bsubtilis ring_color #AAAA00
Bacillaceae.Bacillus.Bthuringiensis ring_color #AAAA00
Bacillaceae.Bacillus.Bweihenstephanensis ring_color #AAAA00
Bacillaceae.Caldalkalibacillus.Cthermarum ring_color #AAAA00
Bacillaceae.Geobacillus.Gkaustophilus ring_color #AAAA00
Bacillaceae.Geobacillus.Gthermodenitrificans ring_color #AAAA00
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_color #AAAA00
Bacillaceae.Lysinibacillus.Lfusiformis ring_color #AAAA00
Bacillaceae.Lysinibacillus.Lsphaericus ring_color #AAAA00
Bacillaceae.Oceanobacillus.Oiheyensis ring_color #AAAA00
Listeriaceae.Listeria.Lgrayi ring_color #AAAA00
Listeriaceae.Listeria.Linnocua ring_color #AAAA00
Listeriaceae.Listeria.Lmonocytogenes ring_color #AAAA00
Listeriaceae.Listeria.Lseeligeri ring_color #AAAA00
Listeriaceae.Listeria.Lwelshimeri ring_color #AAAA00
Paenibacillaceae.Brevibacillus.Bbrevis ring_color #AAAA00
Paenibacillaceae.Brevibacillus.Blaterosporus ring_color #AAAA00
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_color #AAAA00
Paenibacillaceae.Paenibacillus.Plarvae ring_color #AAAA00
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_color #AAAA00
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_color #AAAA00
Paenibacillaceae.Paenibacillus.Pvortex ring_color #AAAA00
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Saureus ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Scapitis ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Scaprae ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Scarnosus ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Sepidermidis ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Shominis ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Slugdunensis ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_color #AAAA00
Staphylococcaceae.Staphylococcus.Swarneri ring_color #AAAA00
Bacillaceae.Anoxybacillus.Aflavithermus ring_alpha 0.486328798075
Bacillaceae.Bacillus.Bamyloliquefaciens ring_alpha 0.902536860011
Bacillaceae.Bacillus.Banthracis ring_alpha 0.540967223446
Bacillaceae.Bacillus.Batrophaeus ring_alpha 0.514745187899
Bacillaceae.Bacillus.Bcellulosilyticus ring_alpha 0.808744341053
Bacillaceae.Bacillus.Bcereus ring_alpha 0.174551783411
Bacillaceae.Bacillus.Bclausii ring_alpha 0.355096857237
Bacillaceae.Bacillus.Bcoagulans ring_alpha 0.30812498305
Bacillaceae.Bacillus.Bcoahuilensis ring_alpha 0.899878301907
Bacillaceae.Bacillus.Bhalodurans ring_alpha 0.135096627341
Bacillaceae.Bacillus.Blicheniformis ring_alpha 0.114946401925
Bacillaceae.Bacillus.Bmegaterium ring_alpha 0.112857448
Bacillaceae.Bacillus.Bmycoides ring_alpha 0.216895687759
Bacillaceae.Bacillus.Bpseudofirmus ring_alpha 0.728546119267
Bacillaceae.Bacillus.Bpseudomycoides ring_alpha 0.862047963812
Bacillaceae.Bacillus.Bpumilus ring_alpha 0.285139149368
Bacillaceae.Bacillus.Bselenitireducens ring_alpha 0.809501074306
Bacillaceae.Bacillus.Bsubtilis ring_alpha 0.261975858288
Bacillaceae.Bacillus.Bthuringiensis ring_alpha 0.887622203873
Bacillaceae.Bacillus.Bweihenstephanensis ring_alpha 0.964470847643
Bacillaceae.Caldalkalibacillus.Cthermarum ring_alpha 0.00503110917306
Bacillaceae.Geobacillus.Gkaustophilus ring_alpha 0.255498806201
Bacillaceae.Geobacillus.Gthermodenitrificans ring_alpha 0.617424889313
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_alpha 0.378606726256
Bacillaceae.Lysinibacillus.Lfusiformis ring_alpha 0.997919879844
Bacillaceae.Lysinibacillus.Lsphaericus ring_alpha 0.707008809187
Bacillaceae.Oceanobacillus.Oiheyensis ring_alpha 0.479214513601
Listeriaceae.Listeria.Lgrayi ring_alpha 0.204916577728
Listeriaceae.Listeria.Linnocua ring_alpha 0.622910173385
Listeriaceae.Listeria.Lmonocytogenes ring_alpha 0.952569768174
Listeriaceae.Listeria.Lseeligeri ring_alpha 0.354875635794
Listeriaceae.Listeria.Lwelshimeri ring_alpha 0.692837888937
Paenibacillaceae.Brevibacillus.Bbrevis ring_alpha 0.580492537793
Paenibacillaceae.Brevibacillus.Blaterosporus ring_alpha 0.67891660613
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_alpha 0.0180110682393
Paenibacillaceae.Paenibacillus.Plarvae ring_alpha 0.953608677163
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_alpha 0.358675673023
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_alpha 0.486438688396
Paenibacillaceae.Paenibacillus.Pvortex ring_alpha 0.186068756014
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_alpha 0.725693055143
Staphylococcaceae.Staphylococcus.Saureus ring_alpha 0.374342186447
Staphylococcaceae.Staphylococcus.Scapitis ring_alpha 0.510175055083
Staphylococcaceae.Staphylococcus.Scaprae ring_alpha 0.948314742048
Staphylococcaceae.Staphylococcus.Scarnosus ring_alpha 0.935701022727
Staphylococcaceae.Staphylococcus.Sepidermidis ring_alpha 0.0938645581046
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_alpha 0.728085338534
Staphylococcaceae.Staphylococcus.Shominis ring_alpha 0.741611869641
Staphylococcaceae.Staphylococcus.Slugdunensis ring_alpha 0.969166259753
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_alpha 0.437648811318
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_alpha 0.781992078475
Staphylococcaceae.Staphylococcus.Swarneri ring_alpha 0.867129362962
Bacillaceae.Anoxybacillus.Aflavithermus ring_color #AA00AA
Bacillaceae.Bacillus.Bamyloliquefaciens ring_color #AA00AA
Bacillaceae.Bacillus.Banthracis ring_color #AA00AA
Bacillaceae.Bacillus.Batrophaeus ring_color #AA00AA
Bacillaceae.Bacillus.Bcellulosilyticus ring_color #AA00AA
Bacillaceae.Bacillus.Bcereus ring_color #AA00AA
Bacillaceae.Bacillus.Bclausii ring_color #AA00AA
Bacillaceae.Bacillus.Bcoagulans ring_color #AA00AA
Bacillaceae.Bacillus.Bcoahuilensis ring_color #AA00AA
Bacillaceae.Bacillus.Bhalodurans ring_color #AA00AA
Bacillaceae.Bacillus.Blicheniformis ring_color #AA00AA
Bacillaceae.Bacillus.Bmegaterium ring_color #AA00AA
Bacillaceae.Bacillus.Bmycoides ring_color #AA00AA
Bacillaceae.Bacillus.Bpseudofirmus ring_color #AA00AA
Bacillaceae.Bacillus.Bpseudomycoides ring_color #AA00AA
Bacillaceae.Bacillus.Bpumilus ring_color #AA00AA
Bacillaceae.Bacillus.Bselenitireducens ring_color #AA00AA
Bacillaceae.Bacillus.Bsubtilis ring_color #AA00AA
Bacillaceae.Bacillus.Bthuringiensis ring_color #AA00AA
Bacillaceae.Bacillus.Bweihenstephanensis ring_color #AA00AA
Bacillaceae.Caldalkalibacillus.Cthermarum ring_color #AA00AA
Bacillaceae.Geobacillus.Gkaustophilus ring_color #AA00AA
Bacillaceae.Geobacillus.Gthermodenitrificans ring_color #AA00AA
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_color #AA00AA
Bacillaceae.Lysinibacillus.Lfusiformis ring_color #AA00AA
Bacillaceae.Lysinibacillus.Lsphaericus ring_color #AA00AA
Bacillaceae.Oceanobacillus.Oiheyensis ring_color #AA00AA
Listeriaceae.Listeria.Lgrayi ring_color #AA00AA
Listeriaceae.Listeria.Linnocua ring_color #AA00AA
Listeriaceae.Listeria.Lmonocytogenes ring_color #AA00AA
Listeriaceae.Listeria.Lseeligeri ring_color #AA00AA
Listeriaceae.Listeria.Lwelshimeri ring_color #AA00AA
Paenibacillaceae.Brevibacillus.Bbrevis ring_color #AA00AA
Paenibacillaceae.Brevibacillus.Blaterosporus ring_color #AA00AA
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_color #AA00AA
Paenibacillaceae.Paenibacillus.Plarvae ring_color #AA00AA
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_color #AA00AA
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_color #AA00AA
Paenibacillaceae.Paenibacillus.Pvortex ring_color #AA00AA
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Saureus ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Scapitis ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Scaprae ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Scarnosus ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Sepidermidis ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Shominis ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Slugdunensis ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_color #AA00AA
Staphylococcaceae.Staphylococcus.Swarneri ring_color #AA00AA
Bacillaceae.Anoxybacillus.Aflavithermus ring_alpha 0.0164337819514
Bacillaceae.Bacillus.Bamyloliquefaciens ring_alpha 0.961779754562
Bacillaceae.Bacillus.Banthracis ring_alpha 0.0911294036676
Bacillaceae.Bacillus.Batrophaeus ring_alpha 0.214683813052
Bacillaceae.Bacillus.Bcellulosilyticus ring_alpha 0.1835464929
Bacillaceae.Bacillus.Bcereus ring_alpha 0.649839771735
Bacillaceae.Bacillus.Bclausii ring_alpha 0.508572486958
Bacillaceae.Bacillus.Bcoagulans ring_alpha 0.54485221387
Bacillaceae.Bacillus.Bcoahuilensis ring_alpha 0.011849863671
Bacillaceae.Bacillus.Bhalodurans ring_alpha 0.494163373827
Bacillaceae.Bacillus.Blicheniformis ring_alpha 0.0037027183784
Bacillaceae.Bacillus.Bmegaterium ring_alpha 0.944619736609
Bacillaceae.Bacillus.Bmycoides ring_alpha 0.740793384052
Bacillaceae.Bacillus.Bpseudofirmus ring_alpha 0.679054870785
Bacillaceae.Bacillus.Bpseudomycoides ring_alpha 0.65485119746
Bacillaceae.Bacillus.Bpumilus ring_alpha 0.696989248748
Bacillaceae.Bacillus.Bselenitireducens ring_alpha 0.250910763296
Bacillaceae.Bacillus.Bsubtilis ring_alpha 0.603110791976
Bacillaceae.Bacillus.Bthuringiensis ring_alpha 0.768995251147
Bacillaceae.Bacillus.Bweihenstephanensis ring_alpha 0.382492089443
Bacillaceae.Caldalkalibacillus.Cthermarum ring_alpha 0.202515841523
Bacillaceae.Geobacillus.Gkaustophilus ring_alpha 0.604966298977
Bacillaceae.Geobacillus.Gthermodenitrificans ring_alpha 0.271415944271
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_alpha 0.729366061868
Bacillaceae.Lysinibacillus.Lfusiformis ring_alpha 0.281874921267
Bacillaceae.Lysinibacillus.Lsphaericus ring_alpha 0.986149233417
Bacillaceae.Oceanobacillus.Oiheyensis ring_alpha 0.0868426043474
Listeriaceae.Listeria.Lgrayi ring_alpha 0.581618564755
Listeriaceae.Listeria.Linnocua ring_alpha 0.587717564353
Listeriaceae.Listeria.Lmonocytogenes ring_alpha 0.520464993313
Listeriaceae.Listeria.Lseeligeri ring_alpha 0.689907782867
Listeriaceae.Listeria.Lwelshimeri ring_alpha 0.432283970377
Paenibacillaceae.Brevibacillus.Bbrevis ring_alpha 0.713859589198
Paenibacillaceae.Brevibacillus.Blaterosporus ring_alpha 0.91882698904
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_alpha 0.0448745597998
Paenibacillaceae.Paenibacillus.Plarvae ring_alpha 0.702703981052
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_alpha 0.365023286887
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_alpha 0.73860888919
Paenibacillaceae.Paenibacillus.Pvortex ring_alpha 0.905904555893
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_alpha 0.252754272893
Staphylococcaceae.Staphylococcus.Saureus ring_alpha 0.483919418674
Staphylococcaceae.Staphylococcus.Scapitis ring_alpha 0.652801998863
Staphylococcaceae.Staphylococcus.Scaprae ring_alpha 0.726258452089
Staphylococcaceae.Staphylococcus.Scarnosus ring_alpha 0.833070576852
Staphylococcaceae.Staphylococcus.Sepidermidis ring_alpha 0.645235993575
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_alpha 0.470807178843
Staphylococcaceae.Staphylococcus.Shominis ring_alpha 0.777865349824
Staphylococcaceae.Staphylococcus.Slugdunensis ring_alpha 0.00619809441301
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_alpha 0.652324807659
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_alpha 0.580610729368
Staphylococcaceae.Staphylococcus.Swarneri ring_alpha 0.243468671906
Bacillaceae.Anoxybacillus.Aflavithermus ring_color #00AAAA
Bacillaceae.Bacillus.Bamyloliquefaciens ring_color #00AAAA
Bacillaceae.Bacillus.Banthracis ring_color #00AAAA
Bacillaceae.Bacillus.Batrophaeus ring_color #00AAAA
Bacillaceae.Bacillus.Bcellulosilyticus ring_color #00AAAA
Bacillaceae.Bacillus.Bcereus ring_color #00AAAA
Bacillaceae.Bacillus.Bclausii ring_color #00AAAA
Bacillaceae.Bacillus.Bcoagulans ring_color #00AAAA
Bacillaceae.Bacillus.Bcoahuilensis ring_color #00AAAA
Bacillaceae.Bacillus.Bhalodurans ring_color #00AAAA
Bacillaceae.Bacillus.Blicheniformis ring_color #00AAAA
Bacillaceae.Bacillus.Bmegaterium ring_color #00AAAA
Bacillaceae.Bacillus.Bmycoides ring_color #00AAAA
Bacillaceae.Bacillus.Bpseudofirmus ring_color #00AAAA
Bacillaceae.Bacillus.Bpseudomycoides ring_color #00AAAA
Bacillaceae.Bacillus.Bpumilus ring_color #00AAAA
Bacillaceae.Bacillus.Bselenitireducens ring_color #00AAAA
Bacillaceae.Bacillus.Bsubtilis ring_color #00AAAA
Bacillaceae.Bacillus.Bthuringiensis ring_color #00AAAA
Bacillaceae.Bacillus.Bweihenstephanensis ring_color #00AAAA
Bacillaceae.Caldalkalibacillus.Cthermarum ring_color #00AAAA
Bacillaceae.Geobacillus.Gkaustophilus ring_color #00AAAA
Bacillaceae.Geobacillus.Gthermodenitrificans ring_color #00AAAA
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_color #00AAAA
Bacillaceae.Lysinibacillus.Lfusiformis ring_color #00AAAA
Bacillaceae.Lysinibacillus.Lsphaericus ring_color #00AAAA
Bacillaceae.Oceanobacillus.Oiheyensis ring_color #00AAAA
Listeriaceae.Listeria.Lgrayi ring_color #00AAAA
Listeriaceae.Listeria.Linnocua ring_color #00AAAA
Listeriaceae.Listeria.Lmonocytogenes ring_color #00AAAA
Listeriaceae.Listeria.Lseeligeri ring_color #00AAAA
Listeriaceae.Listeria.Lwelshimeri ring_color #00AAAA
Paenibacillaceae.Brevibacillus.Bbrevis ring_color #00AAAA
Paenibacillaceae.Brevibacillus.Blaterosporus ring_color #00AAAA
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_color #00AAAA
Paenibacillaceae.Paenibacillus.Plarvae ring_color #00AAAA
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_color #00AAAA
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_color #00AAAA
Paenibacillaceae.Paenibacillus.Pvortex ring_color #00AAAA
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Saureus ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Scapitis ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Scaprae ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Scarnosus ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Sepidermidis ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Shominis ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Slugdunensis ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_color #00AAAA
Staphylococcaceae.Staphylococcus.Swarneri ring_color #00AAAA
Bacillaceae.Anoxybacillus.Aflavithermus ring_height 2.48900854747
Bacillaceae.Bacillus.Bamyloliquefaciens ring_height 2.5569451352
Bacillaceae.Bacillus.Banthracis ring_height 1.4616581923
Bacillaceae.Bacillus.Batrophaeus ring_height 1.5214251868
Bacillaceae.Bacillus.Bcellulosilyticus ring_height 0.275406475474
Bacillaceae.Bacillus.Bcereus ring_height 3.96420929693
Bacillaceae.Bacillus.Bclausii ring_height 0.36682224696
Bacillaceae.Bacillus.Bcoagulans ring_height 3.11304018594
Bacillaceae.Bacillus.Bcoahuilensis ring_height 3.17186920433
Bacillaceae.Bacillus.Bhalodurans ring_height 1.03261323231
Bacillaceae.Bacillus.Blicheniformis ring_height 2.84479580061
Bacillaceae.Bacillus.Bmegaterium ring_height 1.97722308257
Bacillaceae.Bacillus.Bmycoides ring_height 2.66122684072
Bacillaceae.Bacillus.Bpseudofirmus ring_height 1.43290815777
Bacillaceae.Bacillus.Bpseudomycoides ring_height 1.11687288226
Bacillaceae.Bacillus.Bpumilus ring_height 1.08510776094
Bacillaceae.Bacillus.Bselenitireducens ring_height 2.77859614711
Bacillaceae.Bacillus.Bsubtilis ring_height 0.554574632132
Bacillaceae.Bacillus.Bthuringiensis ring_height 1.57378483828
Bacillaceae.Bacillus.Bweihenstephanensis ring_height 2.70028276238
Bacillaceae.Caldalkalibacillus.Cthermarum ring_height 1.86166458022
Bacillaceae.Geobacillus.Gkaustophilus ring_height 0.0242900869783
Bacillaceae.Geobacillus.Gthermodenitrificans ring_height 3.07841560635
Bacillaceae.Geobacillus.Gthermoglucosidasius ring_height 3.46510209264
Bacillaceae.Lysinibacillus.Lfusiformis ring_height 1.35283141925
Bacillaceae.Lysinibacillus.Lsphaericus ring_height 3.92974800987
Bacillaceae.Oceanobacillus.Oiheyensis ring_height 2.28533114154
Listeriaceae.Listeria.Lgrayi ring_height 0.818507572602
Listeriaceae.Listeria.Linnocua ring_height 0.800083345466
Listeriaceae.Listeria.Lmonocytogenes ring_height 0.978937868742
Listeriaceae.Listeria.Lseeligeri ring_height 0.892990893608
Listeriaceae.Listeria.Lwelshimeri ring_height 2.52510303764
Paenibacillaceae.Brevibacillus.Bbrevis ring_height 1.94634642846
Paenibacillaceae.Brevibacillus.Blaterosporus ring_height 2.53149220001
Paenibacillaceae.Paenibacillus.Pcurdlanolyticus ring_height 0.617175345723
Paenibacillaceae.Paenibacillus.Plarvae ring_height 1.49321243619
Paenibacillaceae.Paenibacillus.Pmucilaginosus ring_height 0.0817469468168
Paenibacillaceae.Paenibacillus.Ppolymyxa ring_height 3.26055825675
Paenibacillaceae.Paenibacillus.Pvortex ring_height 2.50175369758
Staphylococcaceae.Macrococcus.Mcaseolyticus ring_height 2.6642090736
Staphylococcaceae.Staphylococcus.Saureus ring_height 1.21391731853
Staphylococcaceae.Staphylococcus.Scapitis ring_height 0.92038173113
Staphylococcaceae.Staphylococcus.Scaprae ring_height 3.22193378354
Staphylococcaceae.Staphylococcus.Scarnosus ring_height 2.59751672494
Staphylococcaceae.Staphylococcus.Sepidermidis ring_height 0.365700208191
Staphylococcaceae.Staphylococcus.Shaemolyticus ring_height 1.34748130999
Staphylococcaceae.Staphylococcus.Shominis ring_height 0.0961524114391
Staphylococcaceae.Staphylococcus.Slugdunensis ring_height 2.02393979902
Staphylococcaceae.Staphylococcus.Spseudintermedius ring_height 1.94654560527
Staphylococcaceae.Staphylococcus.Ssaprophyticus ring_height 2.75289926136
Staphylococcaceae.Staphylococcus.Swarneri ring_height 2.39465498028 Bacillaceae.Bacillus.Bsubtilis clade_marker_label
Staphylococcaceae.Staphylococcus.Saureus clade_marker_label
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
Bacillaceae.Lysinibacillus.Lfusiformis clade_marker_edge_color b
Bacillaceae.Oceanobacillus.Oiheyensis clade_marker_label
Bacillaceae.Oceanobacillus.Oiheyensis clade_marker_color k
Bacillaceae.Oceanobacillus.Oiheyensis clade_marker_font_color w
annot_3.txt
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 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 7.310276093
k__Bacteria 9.278427348
k__Bacteria|p__Acidobacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified 7.389306104
k__Bacteria|p__Chloroflexi 13.67021629
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfococcus|s__Desulfococcus multivorans 5.960850128
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Actinobacteria bacterium 7.53872222
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Cohaesibacteraceae|g__Cohaesibacter 11.39184691
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Pseudoruegeria|s__Pseudoruegeria lutimaris 7.16969386
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Unclassified|s__Desulfobacteraceae bacterium 14.23980864
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_70_13 13.14443874
k__Bacteria|p__Chloroflexi|c__Anaerolineae 13.68106333 2.112284763 8.202129776
k__Bacteria|p__Acidobacteria|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Acidobacteria bacterium 29.01696855
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Rhizobiaceae|g__Rhizobium|s__Rhizobium etli 12.84794764
k__Bacteria|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__bacterium HR39 0.724322421 10.29383757
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Caulobacterales|f__Caulobacteraceae 5.759922595
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 14.54278329
k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Ignavibacteria bacterium RBG_13_36_8 10.05162963
k__Unclassified|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__uncultured prokaryote 9.685375916
k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Marinilabiliales|f__Prolixibacteraceae|g__Draconibacterium 10.88393017
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__SAR86 cluster bacterium 8.946476632
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Unclassified|g__Methyloceanibacter|s__Methyloceanibacter marginalis 9.764440209
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Cellulomonadaceae 1.748909409 3.840517751 16.15571016
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales 12.65760768
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Syntrophobacterales|f__Unclassified|g__Unclassified|s__Syntrophobacterales bacterium RBG_19FT_COMBO_59_10 12.89643047
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Nocardioidaceae|g__Nocardioides 13.22924157
k__Bacteria|p__Actinobacteria|c__Acidimicrobiia|o__Acidimicrobiales|f__Ilumatobacteraceae 8.175966682
k__Bacteria|p__Actinobacteria|c__Thermoleophilia|o__Solirubrobacterales|f__Patulibacteraceae|g__Patulibacter|s__Patulibacter minatonensis 8.41762087
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium 12.2853251
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium RBG_16_52_11 11.90192961
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodospirillales|f__Rhodospirillaceae 9.526283131
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter 8.543885183
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Lysobacter|s__Lysobacter maris 1.466311242 8.33549774
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptosporangiales|f__Thermomonosporaceae|g__Thermomonospora|s__Thermomonospora curvata 34.67083842
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptosporangiales|f__Streptosporangiaceae|g__Thermoactinospora|s__Thermoactinospora rubra 20.59686607
k__Bacteria|p__Acidobacteria|c__Solibacteres|o__Solibacterales|f__Solibacteraceae|g__Candidatus Solibacter|s__Candidatus Solibacter usitatus 25.93679431
k__Bacteria|p__Unclassified|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__bacterium 2.490901843 4.836161424
k__Bacteria|p__Acidobacteria|c__Solibacteres|o__Solibacterales|f__Solibacteraceae|g__Candidatus Sulfopaludibacter|s__Candidatus Sulfopaludibacter sp. SbA3 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 8.109450343
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium CSP1- 8.67399511
k__Bacteria|p__Proteobacteria|c__Candidatus Muproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Candidatus Muproteobacteria bacterium RIFCSPLOWO2_01_FULL_60_18 5.817113316
k__Archaea|p__Thaumarchaeota|c__Nitrososphaeria|o__Nitrososphaerales|f__Nitrososphaeraceae|g__Candidatus Nitrosocosmicus|s__Candidatus Nitrosocosmicus oleophilus 1.307106908 16.0726553
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae 16.64711153
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__delta proteobacterium MLMS- 23.18441205
k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus 21.67229412
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Intrasporangiaceae|g__Phycicoccus 20.59542944
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Mycobacteriaceae|g__Mycobacterium 17.37739359
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium HGW-Chloroflexi- 27.70989789
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Hyphomicrobiaceae|g__Rhodoplanes|s__Rhodoplanes sp. Z2-YC6860 20.55671623
k__Bacteria|p__Proteobacteria|c__Betaproteobacteria 13.80829929
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chloroflexi bacterium HGW-Chloroflexi- 15.83063195
k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Haloferacales|f__Haloferacaceae|g__Halobellus|s__Halobellus limi 7.901859129
k__Bacteria|p__Chlorobi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__Chlorobi bacterium OLB5 0.726510706 11.35743045
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria 33.09793359
k__Bacteria|p__Chloroflexi|c__Unclassified|o__Unclassified|f__Unclassified|g__Unclassified|s__uncultured Chloroflexi bacterium 7.594564607
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter|s__Arthrobacter sp. U41 9.672322849
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhizobiales|f__Unclassified|g__Bauldia|s__Bauldia litoralis 7.811552167
k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Anaerolinea|s__Anaerolinea thermolimosa 5.339928239
k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Anaerolineaceae|g__Longilinea|s__Longilinea arvoryzae 12.65760768
k__Bacteria|p__Bacteroidetes|c__Cytophagia|o__Cytophagales|f__Cyclobacteriaceae|g__Algoriphagus 11.61304782
k__Bacteria|p__candidate division NC10|c__Unclassified|o__Unclassified|f__Unclassified|g__Candidatus Methylomirabilis 11.39184691
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Actinomycetospora|s__Actinomycetospora cinnamomea 5.960850128
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__marine actinobacterium MedAcidi-G2B 11.94948977
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobacter|s__Desulfobacter curvatus 1.422929253 24.26665614
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis 1.64708934 14.04474277
k__Bacteria|p__Chloroflexi|c__Anaerolineae|o__Anaerolineales|f__Unclassified|g__Unclassified|s__Anaerolineales bacterium 4.023842156 3.106301122 6.030977776
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfatitalea|s__Desulfatitalea sp. BRH_c12 14.44036932
k__Bacteria|p__Actinobacteria 8.993563351
Unclassified 12.52506728
k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Unclassified|f__Unclassified|g__Unclassified 10.05162963
k__Bacteria|p__Proteobacteria 33.39629388
k__Bacteria|p__Ignavibacteriae|c__Ignavibacteria|o__Unclassified|f__Unclassified|g__Unclassified|s__Ignavibacteria bacterium RBG_16_34_14 13.20793845
table.txt
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：
source /software/graphlan/activate.sh
export2graphlan.py --skip_rows , -i table.txt --tree tree.txt --annotation annot.txt --most_abundant --abundance_threshold --least_biomarkers --annotations ,,, --external_annotations --min_clade_size
graphlan_annotate.py --annot annot.txt tree.txt abundance.xml
graphlan.py --dpi 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
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