ideogram/scripts/python/convert_gvf_to_annots.py

Chromosome visualization for the web

''' Converts GVF data from dbVar to JSON-formatted annotations'''

import re, json, random

annots = []

chrs = [
    "1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
    "11", "12", "13", "14", "15", "16", "17", "18", "19", "20",
    "21", "22", "X", "Y"
]

lengths_GRCh37 = {
    "1": 249250621, "2": 243199373, "3": 198022430,
    "4": 191154276, "5": 180915260, "6": 171115067,
    "7": 159138663, "8": 146364022, "9": 141213431,
    "10": 135534747, "11": 135006516, "12": 133851895,
    "13": 115169878, "14": 107349540, "15": 102531392,
    "16": 90354753, "17": 81195210, "18": 78077248,
    "19": 59128983, "20": 63025520, "21": 48129895,
    "22": 51304566, "X": 155270560, "Y": 59373566
}

lengths_GRCh38 = {
    "1": 248956422, "2": 242193529, "3": 198295559,
    "4": 190214555, "5": 181538259, "6": 170805979,
    "7": 159345973, "8": 145138636, "9": 138394717,
    "10": 133797422, "11": 135086622, "12": 133275309,
    "13": 114364328, "14": 107043718, "15": 101991189,
    "16": 90338345,	"17": 83257441, "18": 80373285,
    "19": 58617616, "20": 64444167, "21": 46709983,
    "22": 50818468, "X": 156040895, "Y": 57227415
}

file_name = "../data/annotations/estd214_1000_Genomes_Consortium_Phase_3.GRCh38.remap.var.germline.gvf"
file = open(file_name, "r").readlines()

for chr in chrs:
    annots.append({"chr": chr, "annots": []});

for line in file[1:]:
    if line[0] == "#":
        continue

    columns = line.strip().split("\t")

    chr = columns[0]

    # E.g. NC_000001.11 -> 1
    # This RefSeq hack only works for human chromosomes 1-22
    chr = str(int(chr.split(".")[0][-2:]))

    if chr == "23":
    	chr = "X"
    elif chr == "24":
    	chr = "Y"

    if chr not in chrs:
		# E.g. chrMT, alternate loci scaffolds
        continue

    name = ""
    gff_attrs = columns[8].split(";")
    for attr in gff_attrs:
        tmp = attr.split("=")
        if tmp[0] == "Name":
            name = tmp[1]

    start = int(columns[3])
    stop = int(columns[4]) - start

    annot = [
        name,
        start,
        stop,
        1 # placeholder for future use
    ]

    annots[chr]["annots"].append(annot)

annots = json.dumps(annots)
annots = '{"annots":' + annots + '}'

open("../data/annotations/dbvar_estd214.var.json", "w").write(annots)