A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
I'm Lukas, a postdoctoral researcher in the labs of Simon Anders and Ana Martin-Villalba in Heidelberg, Germany. I share Python and R code related to bioinformatics, data science, omics and the occasional fun code project.
Hi, @LKremer
I am trying to use CAFE_fig to visualize the results from CAFE, but I encountered some problems.
Here is my running: python3 ./CAFE_fig/CAFE_fig.py cafe_result.cafe -c asc=vL, da -pb 0.05 -pf 0.05 --dump test/ -g .pdf --count_all_expansions
And these are output:
Traceback (most recent call last):
File "./CAFE_fig/CAFE_fig.py", line 517, in
main(**vars(args))
File "./CAFE_fig/CAFE_fig.py", line 458, in main
c = CAFE_fig(report_cafe, families, clades, pb, pf, dump, gfx_output_format, count_all_expansions)
File "./CAFE_fig/CAFE_fig.py", line 86, in init
self.parse_tree()
File "./CAFE_fig/CAFE_fig.py", line 136, in parse_tree
self.parse_lambdas(line)
File "./CAFE_fig/CAFE_fig.py", line 209, in parse_lambdas
self.lambda_colors[i] = to_rgb(math.log(lambda_), min_l, max_l)
File "./CAFE_fig/CAFE_fig.py", line 62, in to_rgb
v = (v_abs - min_v) / (max_v - min_v) # scaled to a value between 0 and 1
ZeroDivisionError: float division by zero
Could you help with this? I appreciate your help. Thanks!
Fei
Installation process and environment
conda create -n CAFE_fig -c etetoolkit 'ete3==3.0.0b35'
conda list
#
# Name Version Build Channel
blas 1.0 mkl http://mirrors.ustc.edu.cn/anaconda/pkgs/free
cairo 1.14.8 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
certifi 2016.2.28 py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
ete3 3.0.0b35 py35_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
fontconfig 2.12.1 3 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
freetype 2.5.5 2 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
glib 2.50.2 1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
harfbuzz 0.9.39 2 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libffi 3.2.1 1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libgfortran 3.0.0 1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libiconv 1.14 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libpng 1.6.30 1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libxml2 2.9.4 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
libxslt 1.1.29 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
lxml 3.8.0 py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
mkl 2017.0.3 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
numpy 1.13.1 py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
openssl 1.0.2l 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pango 1.40.3 1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pcre 8.39 1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pip 9.0.1 py35_1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pixman 0.34.0 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
pyqt 4.11.4 py35_4 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
python 3.5.4 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
qt 4.8.7 4 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
readline 6.2 2 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
scipy 0.19.1 np113py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
setuptools 36.4.0 py35_1 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
sip 4.18 py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
six 1.10.0 py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
sqlite 3.13.0 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
tk 8.5.18 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
wheel 0.29.0 py35_0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
xz 5.2.3 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
zlib 1.2.11 0 http://mirrors.ustc.edu.cn/anaconda/pkgs/free
I tried the command:
python3 ./CAFE_fig.py example_result.cafe -c Isoptera=zne,mna -pb 0.05 -pf 0.05 --dump test/ -g .pdf --count_all_expansions
Parsing CAFE report... done!
Writing test/summary.pdf
ETE: cannot connect to X server
Cannot work with CAFE version 5.
Hi,
I tried parsing my CAFE resultfile, but got an attribute error. Here is the traceback:
Traceback (most recent call last):
File "../../scripts/CAFE_fig.py", line 509, in
main(**vars(args))
File "../../scripts/CAFE_fig.py", line 454, in main
c.summary_tree()
File "../../scripts/CAFE_fig.py", line 291, in summary_tree
min(self.lambdas.values()), max(self.lambdas.values()))
AttributeError: 'CAFE_fig' object has no attribute 'lambdas'
I am running python on a conda environment with:
pyqt 4.11.4
python 3.5.5
ete3 3.0.0b35
Thanks in advance!
-bash-4.2$ python3 ./CAFE_fig-master/CAFE_fig.py resultfie1.cafe -pb 0.05 -pf 0.05 --dump test/ -g pdf --count_all_expansions
The directory "test/" already exists. Overwrite it and delete all its contents? (y/n)? y
Parsing CAFE report... done!
Writing test/summary.pdf
qt.qpa.screen: QXcbConnection: Could not connect to display
Could not connect to any X display.
could you please help me, thank you very much!
@njliangdong this seems to be an issue with the installation of ete3. Maybe you don't have read and execute permissions in your ete3 installation directory?
i have met the same problem, so do you have any methods to solve it thanks !
Originally posted by @ajkshdkjahdka in #1 (comment)
Hello! When i run the script, i met a problem. The problem:
Parsing CAFE report... done!
Writing test/summary.pdf
qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, minimal, minimalegl, offscreen, vnc, webgl, xcb.
Aborted (core dumped)
This is my code:python3 ./cafe_fig.py example_result.cafe -c Isoptera=zne,mna -pb 0.05 -pf 0.05 --dump test/ -g .pdf --count_all_expansions
The data i used the example.
Thank you very much!!
Hi LKremer
I am trying to use CAFE_fig to visualize the results from CAFE, but I encountered some problems.
Here is my running: python3 ./CAFE_fig-master/CAFE_fig.py out.cafe
And these are output:
Traceback (most recent call last):
File "./CAFE_fig-master/CAFE_fig.py", line 520, in
main(**vars(args))
File "./CAFE_fig-master/CAFE_fig.py", line 461, in main
c = CAFE_fig(report_cafe, families, clades, pb, pf, dump, gfx_output_format, count_all_expansions)
File "./CAFE_fig-master/CAFE_fig.py", line 89, in init
self.parse_tree()
File "./CAFE_fig-master/CAFE_fig.py", line 163, in parse_tree
for family in self:
File "./CAFE_fig-master/CAFE_fig.py", line 334, in iter
yield Family(line, self)
File "./CAFE_fig-master/CAFE_fig.py", line 421, in init
self.pvalue = float(values[2])
ValueError: could not convert string to float: '((Smoellendorffii_1:364.624,(Athaliana_5:314.68,(Earvense_6:251.574,(Dchinensis_2:209.164,(Afokiensis_7:179.207,(((LW_3:55.6774,ZXDS_1:55.6774)_2:46.7325,RS119_1:102.41)_2:39.5235,(Pnudum_4:42.3447,Ttannensis_4:42.3447)_4:99.5887)_3:37.2738)_3:29.9567)_3:42.4098)_3:63.1059)_3:49.944)_3:29.8768,Pp_4:394.5)_3'
Could you help with this? I appreciate your help. Thanks!
Xia
Hello,
I really like this fantastic program to draw Cafe output files. When I used it with my data, the numbers of significantly expanded and contracted families are the same while the example data showed the different numbers. Could you check if this is correct?
Thanks,
Justin
cafe_result.txt
summary.pdf
Conmand line I used:
python ~/softwares/CAFE_fig/CAFE_fig.py -d cafe_fig pan_genome_remove_atalla.cafe
The ete3 information:
pip list
Package Version
------------ --------
asn1crypto 0.24.0
certifi 2019.3.9
cffi 1.11.5
chardet 3.0.4
conda 4.6.14
cryptography 2.4.2
ete3 3.0.0b35
Any suggestions are appreciative !
Dear LKremer,
Thank you for this softeware, while when I run the example date, black and white figure output.
python ./CAFE_fig.py example_result.cafe -c Isoptera=zne,mna -pb 0.05 -pf 0.05 --dump test2/ -g .pdf --count_all_expansions
Hi,
CAFE_fig is cool to plot a gene family tree. When I used CAFE_fig to plot my result of cafe (version=4.2.1), there was an error as follow:
Parsing CAFE report... done!
Writing test/summary.pdf
Traceback (most recent call last):
File "/CAFE_fig/CAFE_fig.py", line 520, in
main(**vars(args))
File "/CAFE_fig/CAFE_fig.py", line 465, in main
c.summary_tree()
File "/CAFE_fig/CAFE_fig.py", line 306, in summary_tree
self.show_or_dump_tree(tree_obj=t, tree_style=ts, fname='summary')
File "/CAFE_fig/CAFE_fig.py", line 410, in show_or_dump_tree
tree_obj.render(out_path, tree_style=tree_style)
File "/Anaconda3/lib/python3.8/site-packages/ete3/coretype/tree.py", line 1392, in render
return drawer.render_tree(self, file_name, w=w, h=h,
File "/Anaconda3/lib/python3.8/site-packages/ete3/treeview/drawer.py", line 104, in render_tree
tree_item, n2i, n2f = render(t, img)
File "/Anaconda3/lib/python3.8/site-packages/ete3/treeview/qt4_render.py", line 254, in render
set_style(n, layout_fn)
File "/Anaconda3/lib/python3.8/site-packages/ete3/treeview/qt4_render.py", line 777, in set_style
func(n)
File "/CAFE_fig/CAFE_fig.py", line 270, in fam_size_piechart_layout
circle_color = self.lambda_colors[node.lambda_group]
AttributeError: 'TreeNode' object has no attribute 'lambda_group'
What is the matter about my result of cafe? Thank you very much!
wang
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