StructureIDs

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Description

A Collection of Go programs to help in the analysis of Structure ID gene pairs.

Prerequisites

• Golang environment.
• .csv files containing Structure ID gene pairs.
• Graphviz or similar installed to visualize fingerprints.

Steps

In order to effectively use these programs, you must use them in order to clean, then analyze the data.

1. Run Vincent_Bypass on the "dirty" data, which are Structure IDs that contain duplicate pairs (ex. gene1, gene1) in the same Structure ID as well as reflected pairs (ex. gene1, gene2 & gene2, gene1). Vincent_Bypass will get rid of duplicated and reflected pairs.
2. On the "cleaned" data, which are the .csv files generated from Vincent_Bypass, run Tita_geneE. You may also run Tita_pinkE on the cleaned data. Both of these programs will find shared pairs between Structure IDs, and will also generate a master file containing all of the shared pairs. Tita_pinkE will contain which Structure IDs the pair is found in the master file.
3. You can also use PairNodes to generate a node graph of the structure pairs and shared genes, this takes in the master file generated from Tita_pinkE
4. Using the cleaned data as well as the master file generated from Tita_geneE, run Tita_chismE. This program will find the pairs which are unique to each StructureID.
5. On the .csv files generated by Tita_chismE, run fingerprints. This program will generate a .dot file, a node graph which contains connectionjs between genes. The .dot file can be visualized in Graphviz or a similar program.

Usage

Each program is already built for linux programs in their respective folders under src. Simply run each program with the necessary flags. To run for windows, navigate to the respective program folder, and run go build. This will generate a .exe file which you can execute using arguments in the command line.

Arguments

Verbose means that it will print out its progress to the terminal.

Vincent_Bypass:

  -i string
    	Directory of "dirty" CSV files to search
  -v	Verbose
  -h  Help

Tita_genE

  -i string
    	Directory of the cleaned CSV Files
  -v	Verbose
  -h  Help

Tita_pinkE

  -i string
    	Directory of the cleaned CSV files
  -v	Verbose
  -h  Help

Tita_chismE

  -i string
    	Directory of where the claned Structure ID files are located
  -m string
    	Directory of the master file containing the shared pairs
  -v	Verbose
  -h  Help

fingerprints

  -i string
    	Directory of .csv files containing unique gene pairs for each Structure ID
  -h  Help

PairNodes

  -i string
    	Master file directory
  -o string
    	Output file
  -v	Verbose