def __init__(self, gtf_index_path, species_id='Homo_sapiens:82'):
"""Load & parse GTF file.
:param gtf_index_path: path to GTF index file
:type gtf_index_path: str
:param species_id: Species code & version of GTF cache to use. E.g.: 'Homo_sapiens:75'
:type species_id: str
"""
assert os.path.exists(gtf_index_path), "Provided path '{}' does not exist!".format(gtf_index_path)
assert gtf_index_path.endswith(
'index'), "Provided index file '{}' does not have *.index suffix. Is it real index?".format(gtf_index_path)
self.logger = logging.getLogger(__name__)
self.species_id, self.gtf_path, self.genes = gtf.get_indexed_genes_for_identifier(gtf_index_path, self.logger,
species_id)
self.genes_indexed_by_id = gtf.index_genes_by_gene_id(self.genes)
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
if __name__ == "__main__":
if options.print_species:
for species in list_indexed_species(options.index):
print species
sys.exit()
#
# get genes previously parsed by index_gtf_files.py
#
if options.verbose >= 2:
logger.log(MESSAGE, "Reading GTF data for %s from %s " % (options.species, options.index))
species, gtf_file_name, genes = get_indexed_genes_for_identifier(options.index, logger, options.species)
if not genes:
raise Exception("No genes for %s from %s" % (options.species, options.index))
if not "protein_coding" in genes:
raise Exception("No protein coding genes for %s" % (options.species,))
if options.print_gene_types:
logger.info("Valid gene types:")
sys.stdout.write("Valid gene types:\n")
for gene_type in sorted(genes.keys()):
sys.stdout.write(" %s\n" % gene_type)
logger.info(" %s\n" % gene_type)
sys.exit()
open_file_names = set()
def get_genes():
logger = logging.getLogger("test")
species_id, gtf_path, genes = gtf_to_genes.get_indexed_genes_for_identifier(
'/Users/poldrack/data_unsynced/selftracking/vega/gtf.index',logger,'Homo_sapiens:59')
return genes
logger.info("Valid gene types in %s / %s:" % (species, gtf_file_name))
sys.stdout.write("Valid gene types in %s (%s):\n" %
(species, os.path.split(gtf_file_name)[1]))
for gene_type in sorted(gene_types):
sys.stdout.write(" %s\n" % gene_type)
logger.info(" %s\n" % gene_type)
sys.exit()
#
# get genes previously parsed by index_gtf_files.py
#
if options.verbose >= 2:
logger.log(
MESSAGE, "Reading GTF data for %s from %s " %
(options.species, options.index))
species, gtf_file_name, genes = get_indexed_genes_for_identifier(
options.index, logger, options.species)
if not genes:
raise Exception("No genes for %s from %s" %
(options.species, options.index))
if not "protein_coding" in genes:
raise Exception("No protein coding genes for %s" % (options.species, ))
open_file_names = set()
#
# output files
#
def open_file(file_name, open_files):
# do not output
if not file_name:
return None
