Repository containing codes used for G-quadruplex studies in mammalian genomes.
Python script used for intersecting G4 coordinates with important genomic features coordinates.
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Input 1: g4 coordinates. Chromosomes should be properly sorted from smaller to larger number (e.g.: chr01-chr24). chromosome start_coord end_coord chr1 123 200
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Input 2: feature coordinates and description. Chromosomes should be properly sorted from smaller to larger number (e.g.: chr01-chr24). chromosome start_coord end_coord description chr1 150 170 GENE_mut1
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Output: overlapped coordinates with overlap size and description from input 2 chromosome start_overlap end_overlap intersection_size description chr1 150 170 21 GENE_mut1
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Usage: python intersect_ok.py input1 input2 output_name
Python script used for assigning a PQS to a single splice site (SS), comparing distance (previously computed) from different splice sites and choosing the shortest distance.
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Input: PQS coordinates in the format below strand gene ss_chr ss_coord pqs_chr pqs_coord distance p ABC chr1 123 chr1 124 +1 p ABC chr1 103 chr1 124 +21
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Output: same format as input, but containing one line per pqs coord, based on distance strand gene ss_chr ss_coord pqs_chr pqs_coord distance p ABC chr1 123 chr1 124 +1
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Usage: Replace arg1 with the name of the input file, and run with "python pqs_closest_to_gene.py".