@transform( (getLongIntervalGeneList, getShortIntervalGeneList, getGeneOverlapGeneList), suffix(".genelist"), ".gtf.gz" )
def getLongIntervalGeneGTF( infile, outfile ):
    gene_file = os.path.join( PARAMS["geneset_dir"], PARAMS["geneset_gene_profile"])
    statement = '''zcat %(gene_file)s 
                   | python %(scriptsdir)s/gtf2gtf.py --filter=gene --apply=%(infile)s --log=%(outfile)s.log
                   | python %(scriptsdir)s/gtf2gtf.py --join-exons --log=%(outfile)s.log
                   | sed s/\\\\ttranscript\\\\t/\\\\texon\\\\t/g 
                   | gzip > %(outfile)s; '''
    P.run()

############################################################
############################################################
## CAPseq profile over long and short capseq interval genes
Filter  GTF file using list of  gene ids associated with long CAPseq intervals
dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_proj007.py/getLongIntervalGeneGTF