def test_build_ensembl_transcript_index(self):
"""Build the gtf portion of the ensembl transcript db
"""
# cat ~/oncotator_pycharm/oncotator/test/testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf | cut -f 9 | cut -f 5 --delimiter=" " | sort | uniq | sed -r "s/;//g" | sed -r "s/\"//g"
# snR84, tK(UUU)K, YAL067C, YAL067W-A, YAL068C, YAL068W-A, YAL069W, YBR278W, YBR279W, YBR280C, YBR281C, YDR528W, YDR529C, YKR074W,
#
# grep -Pzo ">(snR84|tK\(UUU\)K|YAL067C|YAL067W-A|YAL068C|YAL068W-A|YAL069W|YBR278W|YBR279W|YBR280C|YBR281C|YDR528W|YDR529C|YKR074W)([A-Za-z_0-9 \:\-\n]+)" Saccharomyces_cerevisiae.EF4.71.cdna.all.fa >Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa
#
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
output_filename = "out/test_ensembl_gtf.db"
protocol = "file"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], output_filename, protocol=protocol)
self.assertTrue(os.path.exists(output_filename))
shove = Shove(protocol + "://" + output_filename, "memory://")
self.assertTrue(len(shove.keys()) > 0)
self.assertTrue("YDR529C" in shove.keys())
t = shove["YDR529C"]
self.assertTrue(t.get_seq() is not None)
self.assertTrue(t.get_seq() is not "")
self.assertTrue(len(t.get_cds()) > 0)
self.assertTrue(len(t.get_exons()) > 0)
MutUtils.removeDir(output_filename)
def test_build_ensembl_transcript_index(self):
"""Build the gtf portion of the ensembl transcript db
"""
# cat ~/oncotator_pycharm/oncotator/test/testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf | cut -f 9 | cut -f 5 --delimiter=" " | sort | uniq | sed -r "s/;//g" | sed -r "s/\"//g"
# snR84, tK(UUU)K, YAL067C, YAL067W-A, YAL068C, YAL068W-A, YAL069W, YBR278W, YBR279W, YBR280C, YBR281C, YDR528W, YDR529C, YKR074W,
#
# grep -Pzo ">(snR84|tK\(UUU\)K|YAL067C|YAL067W-A|YAL068C|YAL068W-A|YAL069W|YBR278W|YBR279W|YBR280C|YBR281C|YDR528W|YDR529C|YKR074W)([A-Za-z_0-9 \:\-\n]+)" Saccharomyces_cerevisiae.EF4.71.cdna.all.fa >Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa
#
ensembl_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
ensembl_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
output_filename = "out/test_ensembl_gtf.db"
protocol = "file"
genome_build_factory = GenomeBuildFactory()
genome_build_factory.build_ensembl_transcript_index([ensembl_input_gtf], [ensembl_input_fasta], output_filename, protocol=protocol)
self.assertTrue(os.path.exists(output_filename))
shove = Shove(protocol + "://" + output_filename, "memory://")
self.assertTrue(len(shove.keys()) > 0)
self.assertTrue("YDR529C" in shove.keys())
t = shove["YDR529C"]
self.assertTrue(t.get_seq() is not None)
self.assertTrue(t.get_seq() is not "")
self.assertTrue(len(t.get_cds()) > 0)
self.assertTrue(len(t.get_exons()) > 0)
MutUtils.removeDir(output_filename)
def test_build_ensembl_transcripts_by_gene_index(self):
"""Test building an index for getting a transcript given a gene."""
protocol = "file"
transcript_index_filename = "out/test_ensembl_gtf_for_gene.db"
output_filename = "out/test_ensembl_gtf_for_gene.db.gene.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_gene_index(transcript_index_filename, output_filename)
# Now load the index and look something up.
gene_index = Shove(protocol + "://" + output_filename, optimize=False)
self.assertTrue(len(gene_index['SEO1']) == 1)
tx = gene_index['SEO1'][0]
self.assertTrue(tx.get_transcript_id()=="YAL067C")
def test_build_ensembl_transcripts_by_gene_index(self):
"""Test building an index for getting a transcript given a gene."""
protocol = "file"
transcript_index_filename = "out/test_ensembl_gtf_for_gene.db"
output_filename = "out/test_ensembl_gtf_for_gene.db.gene.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_gene_index(transcript_index_filename, output_filename)
# Now load the index and look something up.
gene_index = Shove(protocol + "://" + output_filename, optimize=False)
self.assertTrue(len(gene_index['SEO1']) == 1)
tx = gene_index['SEO1'][0]
self.assertTrue(tx.get_transcript_id()=="YAL067C")
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)
