1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
|
#!/bin/sh
cp annot.txt annot3.txt
# De Filippo
for l in `cat genomes.all.txt | grep g__Prevotella | cut -f 1 | sed -n '0~4p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Xylanibacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Treponema | cut -f 1 | sed -n '0~4p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Butyrivibrio | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
# Yatsunenko
for l in `cat genomes.all.txt | grep s__Streptococcus_alactolyticus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Clostridium.s__leptum | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep s__Clostridium_orbiscindens | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep s__Clostridium_innocuum | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Lactobacillus.s__ruminis | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Eubacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Dialister | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Oscillospira | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
# Clemente
for l in `cat genomes.all.txt | grep g__Helicobacter | cut -f 1 | sed -n '0~6p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Phascolarctobacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Paraprevotella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Anaeroplasma | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Bulleidia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Coprococcus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
#Martinez
for l in `cat genomes.all.txt | grep g__Weissella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Slackia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Gemella | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Streptococcus | cut -f 1 | sed -n '0~14p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Gordonibacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Odoribacter | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
# Obregon
for l in `cat genomes.all.txt | grep g__Succinivibrio | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Catenibacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tg" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Dorea | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Blautia | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Bacteroides | cut -f 1 | sed -n '0~14p'` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Faecalibacterium | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
for l in `cat genomes.all.txt | grep g__Ruminococcus | cut -f 1` ; do echo $l"\tring_width\t2\t8\n"$l"\tring_height\t2\t0.5\n"$l"\tring_shape\t2\tv\n"$l"\tring_color\t2\tr" >> annot3.txt ; done
graphlan_annotate.py DisMic.xml DisMic.annot.xml --annot annot3.txt
graphlan.py DisMic.annot.xml DisMic.png --dpi 200 --size 15 --pad 0.6
graphlan.py DisMic.annot.xml DisMic.svg --dpi 200 --size 15 --pad 0.6
|
