def test_build_ensembl_transcripts_by_genomic_location_index(self):
"""Test that we can get an ensembl transcript from a genomic position"""
protocol = "file"
transcript_index_filename = "out/test_ensemble_gtf_for_gp.db"
output_filename = "out/test_ensemble_gtf_for_gp.db.idx"
shutil.rmtree(output_filename, ignore_errors=True)
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], transcript_index_filename, protocol=protocol)
genome_build_factory.build_ensembl_transcripts_by_genomic_location_index(transcript_index_filename, output_filename, protocol=protocol)
# Now load the index and look something up.
gp_index = Shove(protocol + "://" + output_filename)
gt_transcript_id = "YAL067C"
bins = region2bins(1496172, 1496400)
for bin in bins:
key = 'I_' + str(bin)
if key in gp_index.keys():
self.assertTrue(gp_index[key] == gt_transcript_id)
def test_build_ensembl_transcripts_by_genomic_location_index(self):
"""Test that we can get an ensembl transcript from a genomic position"""
protocol = "file"
transcript_index_filename = "out/test_ensemble_gtf_for_gp.db"
output_filename = "out/test_ensemble_gtf_for_gp.db.idx"
shutil.rmtree(output_filename, ignore_errors=True)
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], transcript_index_filename, protocol=protocol)
genome_build_factory.build_ensembl_transcripts_by_genomic_location_index(transcript_index_filename, output_filename, protocol=protocol)
# Now load the index and look something up.
gp_index = Shove(protocol + "://" + output_filename)
gt_transcript_id = "YAL067C"
bins = region2bins(1496172, 1496400)
for bin in bins:
key = 'I_' + str(bin)
if key in gp_index.keys():
self.assertTrue(gp_index[key] == gt_transcript_id)
