Tuesday, January 24, 2012

First worked tableviewer example

Follow this Link. you should be able to create the picture below.

Note: In windows, there is no cat command, use 'more' instead. Pipe operator still applies in windows. 

A modified tutorial for Windows 7/Vista; first you need to call up strawberry perl terminal and navigate to tableviewer directory

first, create a 3x3 table (use a random seed so that this step is reproducible)
> perl bin\make-table -row 3 -seed 123 -brief > samples\table-basic.txt
# let's see the table
> more samples\table-basic.txt
 lbl    A    B    C
   A  262  209  168
   B   28   86   45
   C   58   95   69
# now parse the table
> more samples\table-basic.txt | bin\parse-table > tmp.txt
# now create configuration and data files
> more tmp.txt | bin\make-conf -dir data
# let's see what was created
> dir data/
 Directory of c:\circos-0.55\tools\tableviewer\data

01/24/2012  10:35 PM    <DIR>          .
01/24/2012  10:35 PM    <DIR>          ..
01/24/2012  10:35 PM               255 all.txt
01/24/2012  10:35 PM               261 cap.col.txt
01/24/2012  10:35 PM               247 cap.row.txt
01/24/2012  10:35 PM               740 cells.txt
01/24/2012  10:35 PM               255 col.txt
01/24/2012  10:35 PM                62 colors.conf
01/24/2012  10:35 PM               598 colors_percentile.conf
01/24/2012  10:35 PM                72 karyotype.txt
01/24/2012  10:35 PM               249 row.txt
01/24/2012  10:35 PM                48 scaling.conf
01/24/2012  10:35 PM                33 segmentlabel.txt
              11 File(s)          2,820 bytes
               2 Dir(s)  20,571,529,216 bytes free
# now draw the image (circos.conf is already defined to use the data files from data/) (suppose you are still in 'tableviewer' directory
> perl ..\..\bin\circos -conf etc/circos.conf -outputfile table-basic.png