Circos for comparative genomes

szypanther — Tue, 15 Jan 2013 08:03:30 +0000

Circos:
nucmer –prefix=refBAV1_qryVScds Dehalococcoides_BAV1.fasta Dehalococcoides_VS.cds.fasta
show-tiling -i 80 -c refBAV1_qryVScds.delta > refBAV1_qryVScds.tiling
awk -F ” ” ‘{print “chr1″ “\t” $1 “\t” $2}’ refBAV1_qryVScds.tiling > Dehalococcoidessp.VScds.gene_tableBAV1.txt

shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/circos/circos-tutorials-0.62/tutorials/8/1$ perl ../../../../circos-0.62-1/bin/circos -conf circos.conf

shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/circos/circos-tutorials-0.62/tutorials/8/1$ ll
total 16001
-rwxrwxrwx 1 root root 528519 2012-12-27 16:11 circos1.png
-rwxrwxrwx 1 root root 1065925 2012-12-27 14:33 circos2.png
-rwxrwxrwx 1 root root 1230394 2013-01-15 14:04 circosBAV1_VS11a_genome.jpg
-rwxrwxrwx 1 root root 4654 2013-01-15 13:11 circos.conf
-rwxrwxrwx 1 root root 1119210 2013-01-15 13:36 circos.jpg
-rwxrwxrwx 1 root root 794858 2013-01-15 13:15 circos.png
-rwxrwxrwx 1 root root 2900177 2013-01-15 13:15 circos.svg
-rwxrwxrwx 1 root root 4242152 2013-01-15 13:32 circos.xcf
-rwxrwxrwx 1 root root 4242152 2013-01-15 13:30 circos.xcf.png
-rwxrwxrwx 1 root root 128 2013-01-14 15:01 highlights.conf
-rwxrwxrwx 1 root root 2075 2013-01-14 14:42 highlights.conf.org
-rwxrwxrwx 1 root root 892 2013-01-15 13:15 ideogram.conf
-rwxrwxrwx 1 root root 35132 2011-03-22 00:40 image-01.png
-rwxrwxrwx 1 root root 30883 2011-03-22 00:40 image-02.png
-rwxrwxrwx 1 root root 126878 2011-03-22 00:40 image-03.png
-rwxrwxrwx 1 root root 1305 2012-05-05 00:25 ticks.conf

circos.conf

ideogram.conf

Dehalococcoidessp.BAV1.gene_table2

Dehalococcoidessp.11a.gene_tableBAV1

Dehalococcoidessp.GTcds.gene_tableBAV1

karyotype.microbe

Dehalococcoidessp.CBDB1cds.gene_tableBAV1

Dehalococcoidessp.195cds.gene_tableBAV1

Circos 安装和学习（一）

szypanther — Thu, 06 Sep 2012 02:33:59 +0000

http://circos.ca/documentation/

Tutorials and Course

The tutorials serve as a walkthrough through Circos. The course is a more structured set of materials that takes you through creating an image from scratch.

The tutorials act as documentation — each lesson presents a specific feature of Circos.

Example Image

Once you download and install Circos,

# install circos
> tar xvfz circos-x.xx.tgz
> cd circos-x.xx

If you get an error like

-bash: /bin/env: No such file or directory

then your 'env' binary is likely in /usr/bin (e.g. on Mac OS X) Check this by 

> which env
/usr/bin/env

To fix this, either change the first line in scripts in bin/* and tools/*/bin to 

#!/usr/bin/env perl

or make a symlink from /usr/bin/env to /bin/env

> sudo su
> cd /bin
> ln -s /usr/bin/env env

files

file	version	size	date	comment
current
circos-tools-0.16-1.tgz	0.16	13,721,840	Wed Aug 1 17:38:27 2012	circos-tools-0.16-1.tgz is a bug release.
circos-0.62-1.tgz	0.62	23,776,624	Tue Jul 3 12:59:00 2012	circos-0.62-1.tgz is a bug release.
circos-0.62.tgz	0.62	21,905,722	Mon Jun 25 15:30:13 2012
circos-tutorials-0.62.tgz	0.62	125,634,176	Mon Jun 25 14:49:15 2012
circos-course-0.61.tgz	0.61	325,718,042	Tue Jun 5 15:15:03 2012
circos-tools-0.16.tgz	0.16	11,046,936	Mon Jul 25 14:29:13 2011

下载解压后还需要安装一些Circos依赖的必要模块等：

Config::General (v2.50 or later)
GD
GD::Polyline
List::MoreUtils
Math::Bezier
Math::Round
Math::VecStat
Params::Validate
Readonly
Regexp::Common
Set::IntSpan (v1.16 or later)
Text::Format
Font::TTF::Font
利用CPAN自行安装以上模块

安装模块

perl -MCPAN -e shell
cpan> install Math::Bezier
cpan> install Regexp::Common

……

try creating the example image that ships with the Circos core distribution.

> cd example
# on UNIX systems (see README for Windows use)
> ./run

Creating a Tutorial Image

You will need to download the tutorials separately. Follow the installation instructions in the archive file.

> cd tutorials/2/2
# now try tutorial 2.2
> ../../../bin/circos -conf ./circos.conf

俺的安装路径如下：
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/circos/circos-tutorials-0.62/tutorials/2/2$ ../../../../circos-0.62-1/bin/circos -conf ./circos.conf
debuggroup conf 0.13s welcome to circos v0.62-1 25 Jun 2012
debuggroup conf 0.13s loading configuration from file ./circos.conf
debuggroup conf 0.13s looking for conf file ./circos.conf
debuggroup conf 0.13s found conf file ./circos.conf
debuggroup summary 0.32s debug will appear for these features: summary
debuggroup summary 0.32s parsing karyotype and organizing ideograms
debuggroup summary 0.49s applying global and local scaling
debuggroup summary 0.50s allocating image, colors and brushes
debuggroup summary 5.91s drawing highlights and ideograms
debuggroup summary,output 8.10s generating output
debuggroup summary,output 8.77s created PNG image ./circos.png (605 kb)
debuggroup summary,output 8.77s created SVG image ./circos.svg (371 kb)

Circos INSTALL SUCCESS!

小生这厢有礼了(BioFaceBook Personal Blog) » Circos