Utility Scripts

#Utility Scripts

There have been several scripts to help the user interact with the files required for input or produced by the tool as output. These scripts are located in the bin folder. I have plans to add a significant amount of functionality to these tools over the next year. Overall the use of the scripts can be determined by their names and the usage of the tools can be determined by setting looking at the top of the scripts. There are plans to improve the interfaces to these tools and hopefully consolidate several off them.

##convert_gistic_to_obs_file.pl

This scripts takes in copy number data produced by the Gistic tool and creates a observation file with all the nodes that are within a particular database

###Usage

Specify file paths within the script

Command: perl convert_gistic-to-obs.pl <gistic-file> > <output-path>

###Gistic file

####Format:

Unique.Name  NC_full NC_partial Coding_full Coding_partial CDS_overlaps <sample1 >... <sample n>

The first column (Unique.Name) is expected to the region name contain and the following 4 columns (NC_full NC_partial Coding_full Coding_partial) are expected to have lists of genes that are comma separated and surrounded by quotes. The gene names are expected to be Uniprot (HUGO) Gene names.

##DB ID to name mapping file

This file should be provided by Reactome. We are currently setting up a systematic way to distribute these files.

####Format:

 NodeID  NodeName ReactomeType