def __get_binned_data(self, chr, start, end, type):
if type == "gene":
data = self.Genes
elif type == "transcript":
data = self.Transcripts
# GAF uses M_rCRS whereas mutations are often using M for the chromosome field.
if chr == "M" and ("M" not in data) and ("M_rCRS" not in data):
raise GafInvalidChromosomeValue(
"Unable to process mitochondria mutation with chr: %s .... data keys are %s" % (str(chr)),
str(data.keys()),
)
if chr == "M" and ("M" not in data):
# TODO: Verify that it is okay to do this.
chr = "M_rCRS"
if chr not in data:
self.logger.warn("Invalid chromosome value for Gaf search: %s" % (str(chr)))
return list()
# raise GafInvalidChromosomeValue("Invalid chromosome value: %s" % (str(chr)))
bins = region2bins(start, end)
records = list()
for b in bins:
records.extend(data[chr].get(b, []))
return records
def __get_binned_data(self, chr, start, end, type):
if type == 'gene':
data = self.Genes
elif type == 'transcript':
data = self.Transcripts
# GAF uses M_rCRS whereas mutations are often using M for the chromosome field.
if chr == 'M' and ('M' not in data) and ('M_rCRS' not in data):
raise GafInvalidChromosomeValue(
"Unable to process mitochondria mutation with chr: %s .... data keys are %s"
% (str(chr)), str(data.keys()))
if chr == 'M' and ('M' not in data):
# TODO: Verify that it is okay to do this.
chr = 'M_rCRS'
if chr not in data:
self.logger.warn("Invalid chromosome value for Gaf search: %s" %
(str(chr)))
return list()
#raise GafInvalidChromosomeValue("Invalid chromosome value: %s" % (str(chr)))
bins = region2bins(start, end)
records = list()
for b in bins:
records.extend(data[chr].get(b, []))
return records
def _get_binned_transcripts_given_index(self, chr, start, end, index_dict):
bins = region2bins(int(start), int(end))
records = list()
for b in bins:
key = chr + "_" + str(b)
try:
txs = index_dict[key]
records.extend(txs)
except KeyError:
pass
return set(records)
def _get_binned_transcripts_given_index(self, chr, start, end, index_dict):
bins = region2bins(int(start), int(end))
records = list()
for b in bins:
key = chr + "_" + str(b)
try:
txs = index_dict[key]
records.extend(txs)
except KeyError:
pass
return set(records)
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)