Question: Error: Circos Plot Creating In Windows Perl (First Time User Problem)
1
gravatar for John
7.5 years ago by
John1.5k
John1.5k wrote:

I am using the activeperl in my windows. I am trying to repeat a tutorial exercise to make myself confidence that I can do myself after some extra days effort.

cd   c:\Perl64\bin\

c:\Perl64\bin perl -conf C:\Users\Owner\Desktop\circos\ circos.2.conf 
 -outputdir C:\Users\Owner\Desktop\circos\     -outputfile firsttrial.png

perl.exe is under the dictory C:\Perl64\bin. the circos.2.conf file is the directory specified above.

I created "circos.2.conf" by coping the text from the circos website. I just changed " data/6/histogram.txt" to "Users\Owner\Desktop\circos\histogram.txt" to meet my interest and the file is stored in the same folder as circos.2.conf. I am not sure where I need to use "/" or "\" for directory - linux or windows convention.

<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.2.conf>>
<<include ticks.2.conf>>

karyotype = Users\Owner\Desktop\circos\karyotype.human.txt

<image>
dir = /tmp
file  = circos-tutorial.png
# radius of inscribed circle in image
radius         = 1500p
background     = white
angle_offset   = -90
</image>

chromosomes_units = 1000000

chromosomes_display_default = yes

#chromosomes = hs1;hs2;hs3;hs4;hs5;hs6

<plots>

<plot>

file = Users\Owner\Desktop\circos\histogram.txt
type = histogram

r0 = 0.8r
r1 = 0.9r

min=0.15
max=0.3

color     = black
fill_under = yes
fill_color = green
thickness = 2

extend_bin = no

axis           = yes
axis_color     = lgrey
axis_thickness = 2
axis_spacing   = 0.1

background       = yes
background_color = lgreen
background_stroke_color = black
background_stroke_thickness = 2

</plot>

<plot>

file = Users\Owner\Desktop\circos\histogram.txt
type = histogram

r0 = 0.6r
r1 = 0.7r

min=-0.3
max=-0.15

color     = black
fill_under = yes
fill_color = red
thickness = 2

extend_bin = no

axis           = yes
axis_color     = lgrey
axis_thickness = 2
axis_spacing   = 0.1

background       = yes
background_color = lred
background_stroke_color = black
background_stroke_thickness = 2

</plot>

<plot>

file = Users\Owner\Desktop\circos\histogram.txt
type = histogram

r0 = 0.7r
r1 = 0.8r

min=-0.15
max=0.15

color     = black
fill_under = yes
fill_color = orange
thickness = 2

extend_bin = no

axis           = yes
axis_color     = lgrey
axis_thickness = 2
axis_spacing   = 0.1

background       = yes
background_color = lorange
background_stroke_color = black
background_stroke_thickness = 2

</plot>

</plots>

anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

# don't touch!
units_ok        = bupr
units_nounit    = n

Thus my directory has following files: conf file, histogram.txt and karyotype.human.

c:\Perl64\bin>perl -conf C:\Users\Owner\Desktop\circos\    circos.2.conf -output
dir C:\Users\Owner\Desktop\circos\     -outputfile firsttrial.png

EROR MESSAGE !!!!

Unrecognized switch: -onf  (-h will show valid options).

What is this message ? I did not get any output to my C:\Users\Owner\Desktop\circos\, am I close ???? sorry for basic question

perl windows graphs • 3.8k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 7.5 years ago by John1.5k
3

looks like u simply forgot to load enter the perl script on your command line, and the error means that perl doesn't have the -conf option (I think the perl script is named circos, or circos.pl) : perl circos -conf C:UsersOwnerDesktopcircoscircos.2.conf -output dir C:UsersOwnerDesktopcircos -outputfile firsttrial.png

ADD REPLYlink written 7.5 years ago by Michael Dondrup46k

Why don't you use CIRCOS online http://mkweb.bcgsc.ca/tableviewer/

ADD REPLYlink written 7.5 years ago by Dataminer2.6k

good suggestion, is every type of CIRCOS plot possible online ?? that is my motivation to learn it ...

ADD REPLYlink written 7.5 years ago by John1.5k

Paraphrasing from the Circos Table Viewer website: the visualizations shown there are created by the tableviewer utility script, which is included in Circos. The web page provides a limited interface to the tableviewer (and Circos). For full functionality you need to download it and run it locally.

ADD REPLYlink written 7.5 years ago by Obi Griffith18k

thanks for the suggestions, see my recent edits ...looks like the program is running but there is file deficiency, I do not know where I can find it

ADD REPLYlink written 7.5 years ago by John1.5k

I tried to edit the question, but could not so please see the edits as answer ..."ideogram.2.conf" is not available ...i do not know where I can find it

ADD REPLYlink written 7.5 years ago by John1.5k
1
gravatar for John
7.5 years ago by
John1.5k
John1.5k wrote:

I could not edit my question, so here is partial solution, but there is still bug remaining

c:\Perl64\bin>perl  C:\circos\circos-0.55\circos-0.55\bin\circos -conf C:\Users\
Owner\Desktop\circos\circos.2.conf -outputdir C:\Users\Owner\Desktop\circos\ -ou
tputfile firsttrial.png

Config::General The file "ideogram.2.conf" does not exist within ConfigPath: C:\
Users\Owner\Desktop\circos\.C:\Users\Owner\Desktop\circos.C:\Users\Owner\Desktop
\circos/etc.C:/circos/circos-0.55/circos-0.55/bin/etc.C:/circos/circos-0.55/circ
os-0.55/bin/../etc.C:/circos/circos-0.55/circos-0.55/bin/...C:/circos/circos-0.5
5/circos-0.55/bin! at C:/circos/circos-0.55/circos-0.55/bin/../lib/Circos/Config
uration.pm line 381
ADD COMMENTlink written 7.5 years ago by John1.5k

I found the following notes interesting

http://genomevisualization.net/tutorials/course/handouts/circos-s2.pdf

ADD REPLYlink written 7.5 years ago by John1.5k

I found the ideogram.2.conf file.

http://mkweb.bcgsc.ca/template/circos/tutorials/lessons/2d_tracks/histograms/configuration/

ADD REPLYlink written 7.5 years ago by John1.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 800 users visited in the last hour