creation of gffutils database from Gencode v19 annotations

gencode-db.py

import gffutils
import datetime

# Annotations from:
# ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz

v19gff = 'gencode.v19.annotation.gtf'
v19db_filename = v19gff + '.db'
gene_transcript = set(('gene', 'transcript'))


def transform(f):
    if f.featuretype in gene_transcript:
        return f
    else:
        exon_location = '{}:{}:{}-{}:{}'.format(f.featuretype, f.seqid, f.start, f.stop, f.strand)
        exon_id = exon_location
        if f.featuretype == 'CDS':
            exon_id += ':' + f.frame
        f.attributes['fancy_id'] = [exon_id]
        return f

print datetime.datetime.now()
v19db = gffutils.create_db(
    v19gff,
    v19db_filename,
    merge_strategy='merge',
    id_spec={'gene': 'gene_id', 'transcript':
             'transcript_id','exon':'fancy_id',
             'CDS':'fancy_id','start_codon':'fancy_id',
             'stop_codon':'fancy_id','UTR':'fancy_id'},
    transform=transform,
    force=True,
    verbose=True,
    infer_gene_extent=False,
    force_merge_fields=['source'])
print datetime.datetime.now()