2.2.4.1 Scripts for automated data generation

Array files can be generated by the script vampTxt2xml. As an input, this script takes csv (comma separated value) text files. The field names must correspond to the tags listed in section 2.2.4 and the file must be ordered by chromosome and position. We give an example of such an input file below:

Y,X,Chr,Name,Smt,Bkp,Out,Gnl,Weight
1.658040e-01,3247817,1,RP4-785P20,-0.020635750,0,0,0,NA
1.316050e-01,4487199,1,RP1-37J18,-0.020635750,0,0,0,NA
-9.597111e-02,5877818,1,RP11-49J3,-0.020635750,0,0,0,NA
3.588748e-02,7071571,1,RP3-438L4,-0.020635750,0,0,0,NA
-1.012979e-01,7653186,1,RP11-338N10,-0.020635750,0,0,0,NA
-1.728830e-01,9146799,1,RP3-510D11,-0.020635750,0,0,0,NA
5.558425e-02,10087260,1,RP4-575L21,-0.020635750,0,0,0,NA
.
.

This script outputs array files in the following directory structure:

• a first subdirectory structure contains pan-genomic profile of each array and chromosomic profile of all arrays in the project $[$project_name$]$ (this subdirectory structure is used for Import functions)

  /[project_name]/array/[array_name].xml
                  chr/chr01.xml
                  .
                  .
                  .
                  chr/chrY.xml
  

• a second subdirectory structure contains chromosomic profile of all arrays in all projects ( this subdirectory structure is used for Save and Load functions)

  /all/chr01/[array_name].xml                
       .
       .
       .
       chrY/[array_name].xml
  

The script vampProject2import automatically generates an import file based on the previous directory structure. An example of such an import file is given in the Annexes (see 8.3).