Re: [circos] Error in Creating Karyotype

[Martin Krzywinski]

Hi Ben,

You need to use the -conf flag to specify the configuration file.

> bbgreen$ perl -conf /Applications/circos-0.55/other/circos.conf

Your configuration file looks like it's from an older version of
Circos. There have been quite a few changes in v0.6x and I suggest
that you use the latest version of Circos to avoid compatibility
problems in the future.

In the new version you'll find the bovine karyotype file in

data/karyotype/assembly/karyotype.cow.txt

which is based on the Oct 2011 (4.6.1) version. I've attached it here
(colors for chromosomes chr25+ are not defined by default in Circos,
which only defines the human chromosome palette used by UCSC - see
README).

Martin Krzywinski
science + art
http://mkweb.bcgsc.ca



On Mon, Sep 17, 2012 at 11:10 AM, Ben Green <bbgre...@gmail.com> wrote:
> Hi all,
>
> This is likely a basic issue, but when trying to create a karyotype of the
> bovine genome I am running into some issues within Perl. I have created a
> karyotype.cow.conf file and am using the format from the Circos site but am
> getting the following errors:
>
> bbgreen$ perl /Applications/circos-0.55/other/circos.conf
>
> Bareword found where operator expected at
> /Applications/circos-0.55/other/circos.conf line 3, near "</colors"
> (Might be a runaway multi-line // string starting on line 2)
> (Missing operator before lors?)
> syntax error at /Applications/circos-0.55/other/circos.conf line 3, near
> "</colors"
> Can't find string terminator "include" anywhere before EOF at
> /Applications/circos-0.55/other/circos.conf line 9.
>
> The following is my circus.conf code if that helps figure out where I am
> going wrong (I have moved some .conf files from /etc to a folder I created
> (other) for organization):
>
> <colors>
> <<include other/colors.conf>>
> </colors>
>
> <fonts>
> <<include other/fonts.conf>>
> </fonts>
>
> <<include ideogram.conf>>
> <<include ticks.conf>>
>
>
> karyotype = other/karyotype.cow.txt
>
> <image>
> dir = /tmp
> file = circos-tutorial.png
> # radius of inscribed circle in image
> radius = 1500p
> background = white
> # by default angle=0 is at 3 o'clock position
> angle_offset = -90
> #angle_orientation = counterclockwise
> </image>
>
> chromosomes_units = 1000000
>
> #chromosomes_display_default = yes
>
> chromosomes = hs1;hs2;hs3
>
> anglestep = 0.5
> minslicestep = 10
> beziersamples = 40
> debug = no
> warnings = no
> imagemap = no
>
> units_ok = bupr
> units_nounit = n
>
>
>
> Any help is greatly appreciated.
>
> -Ben
>
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[Ben Green]

Hi Martin,

Perfect. That fixed the issue. I appreciate the help.

Ben