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  • Finding Tripartite Data Groups for microRNA-TF-Gene Regulatory Circuits

    I'm pretty new to the world of scripting and have a problem in my research lab that, if a script could be written, would have days worth of manual labor and graciously ask for the community's assistance in how I could go about writing a Python or perhaps a Perl script to solve this problem. Any assistance or direction would be GREATLY appreciated!

    In the attachment I have a file with four columns as input data, where $1 and $2 essentially come as a pair and $3 and $4 also come as pairs. However, I want to find three-way triplet (tripartite) graph relationships within the data such that there are two main types present:
    Type 1) TF --> Gene <-- mir <-- TF
    Type 2) miR --> Gene <-- TF <-- miR

    This could be broken into two different scripts if need be:

    For the first script (Type 1)
    Print TF
    IF TF present in $TF twice
    AND Target present BOTH in one row of $miR and $Gene
    THEN print miR and Gene in question as miR and Gene
    THEN print 1 in $Type

    For the second script (Type 2)
    Print miR
    IF miR present in $miR twice
    AND Gene present BOTH in one row of $TF and $Target
    THEN print TF and Target in question as TF and Gene
    THEN print 2 in $Type

    The attachment has both input and what I hope to receive as output.
    Attached Files

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