satisfying criteria categorize_elements_satisfying_criteria.pl $inputFile1 $inputFile2 $outputFile1

.. class:: infomark **What it does** The program takes as input a set of categories, such that each category contains many elements. It also takes a table relating elements with criteria, such that each element is assigned a number representing the number of times the element satisfies a certain criterion. - The first input is a TABULAR format file, such that the left column represents the names of categories and, all other columns represent the names of elements in each category. - The second input is a TABULAR format file relating elements with criteria, such that the first line represents the names of criteria and the left column represents the names of elements. - The output is a TABULAR format file relating catergories with criteria, such that each categoy is assigned a number representing the total number of times its elements satisfies a certain criterion.. Each category is assigned as many numbers as criteria. **Example** Let the first input file be a group of motif categories as follows:: Deletion_Hotspots deletionHoptspot1 deletionHoptspot2 deletionHoptspot3 Dna_Pol_Pause_Frameshift dnaPolPauseFrameshift1 dnaPolPauseFrameshift2 dnaPolPauseFrameshift3 dnaPolPauseFrameshift4 Indel_Hotspots indelHotspot1 Insertion_Hotspots insertionHotspot1 insertionHotspot2 Topoisomerase_Cleavage_Sites topoisomeraseCleavageSite1 topoisomeraseCleavageSite2 topoisomeraseCleavageSite3 And let the second input file represent the number of times each motif occurs in a certain window size of indel flanking regions, as follows:: 10bp 20bp 40bp deletionHoptspot1 1 1 2 deletionHoptspot2 1 1 1 deletionHoptspot3 0 0 0 dnaPolPauseFrameshift1 1 1 1 dnaPolPauseFrameshift2 0 2 1 dnaPolPauseFrameshift3 0 0 0 dnaPolPauseFrameshift4 0 1 2 indelHotspot1 0 0 0 insertionHotspot1 0 0 1 insertionHotspot2 1 1 1 topoisomeraseCleavageSite1 1 1 1 topoisomeraseCleavageSite2 1 2 1 topoisomeraseCleavageSite3 0 0 2 Running the program will give the total number of times the motifs of each category occur in every window size of indel flanking regions:: 10bp 20bp 40bp Deletion_Hotspots 2 2 3 Dna_Pol_Pause_Frameshift 1 4 4 Indel_Hotspots 0 0 0 Insertion_Hotspots 1 1 2 Topoisomerase_Cleavage_Sites 2 3 4