Description

The parser transforms the exported ASCII raw data from the Applied Imaging system v.3.01 (from 1995) in a vector like format usable to be easily imported in e.g. R or LibreOffice.
Optional the blanking of the centromer and none evaluable regions might be performed during the conversion process.

see ODF table: measurements and mapping to the chromosomal regions (24 KB)

Some features of the program:
-creating one output file for all experiments (or one file per experiment)
-building means from up to two measurements on one 'slide'
-replacing the decimal dot by a comma (european format)

Install a MONO runtime on Debian/Ubuntu

In short:

$ sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF
$ echo "deb https://download.mono-project.com/repo/debian wheezy main" | sudo tee /etc/apt/sources.list.d/mono-xamarin.list
$ sudo apt-get update
$ sudo apt-get install mono-complete

For coding issues you need additionally:

$ sudo apt-get install monodevelop mono-vbnc

In the case of problems look at the MONO web site.

Formats

Input

CGH ratio data in blocks, 8 in a row, some chromosomes might be missing
Data from such a folder, e.g.: /.../3651/slide0/cell9/cgh.rats

2 182
0.928207 0.928207 0.928207 1.012871 1.012871 1.040374 1.040374 1.040374
.....
1.073986 1.036183 1.036183 1.123358 1.123358 1.431219

2 182
0.892525 0.892525 0.892525 0.986438 0.986438 0.994899 0.994899 0.960951
.....
1.049657 1.049657 1.200850 1.200850 1.389061 1.000000

3 154
1.023162 1.023162 1.023162 0.993290 0.993290 0.993290 1.001561 1.001561
.....
0.979005 0.979005 0.916921 0.916921 0.832465 0.832465 0.832465 0.781722
0.781722 0.967822

3 154
0.904337 0.904337 0.904337 1.000224 1.000224 0.990892 0.990892 0.946762
.....
1.074098 1.074098 1.078660 1.078660 1.231315 1.231315 1.231315 1.304888
1.304888 1.406623

4 144
1.558542 1.558542 1.558542 1.463850 1.463850 1.463850 1.260583 1.260583
.....
0.731537
.....

Output

In the case of mean: 1..2099 containing sequentially the chromosomes 1,2,3, ... to X and Y.
e.g.:
1,166037;
1,166037;
.....
1,000000;
1,000000;

Chromosomes which are left out during data generation are filled with '0's in the vector.

In the other case: 1..4198 containing the chromosomes 1,1,2,2,3,3, ... to X,X and Y,Y.

Bulk files will have a header row (therefore 1..4199 rows).
e.g.:
c3651x08;c3651x09;
1,166037;0;
1,166037;0;
.....