change_the_name.py

class stat:
    def __init__(self,INFO):
        self.DESCRIPTION =  ['Demo for harmbrugge', 'ENSMUSG00000051951'] 
        self.LINKABLE = True 
        self.SQL = 'TEXT'
        self.dependencies = ['CHR','POS','SEQ']
        self.before = '''
import intervaltree
GTF_chromosomes = {}
with open('/Users/John/Downloads/Mus_musculus.GRCm38.86.gtf','rb') as f:
    for line in f:
        line = line.split('\t')
        if len(line) < 9: continue
        chr = line[0]
        start = int(line[3])
        end = int(line[4]) + 1         # My GTF file has 0-length entries and intervaltree doesn't like that. So I +1. I don't know your formatting.
        name = line[8].split('"')[1]   # This extracts the first field in the 9th column for my GTF, which is the name. Yours might be different..? 
        if chr not in GTF_chromosomes: GTF_chromosomes[chr] = intervaltree.IntervalTree()
        GTF_chromosomes[chr][start:end] = name
'''
        self.METHOD = '''
try: GTF = ','.join(set([ x[2] for x in GTF_chromosomes[CHR][POS:POS+len(SEQ)] ]))
except KeyError: GTF = 'Unknown Chromosome'
'''
addStat('GTF',[])