def test_simple_genes_by_region_annotation(self):
"""Test web api backend call /genes/ """
# http://www.broadinstitute.org/oncotator/genes/chr22_22112223_22312558/
# Two genes: chr22:22,112,223-22,312,558
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
# Here is what the API would call....
txs = annotator.retrieve_transcripts_by_region("22", 22112223, 22312558)
self.assertTranscriptsFound(txs)
mut_dict = annotator.annotate_genes_given_txs(txs)
# Each mut will be for a separate gene
for gene in mut_dict.keys():
mut = mut_dict[gene]
alt_accessions = mut["UniProt_alt_uniprot_accessions"].split("|")
tcgascape_amp_peaks = mut["TCGAScape_Amplification_Peaks"].split("|")
tcgascape_del_peaks = mut["TCGAScape_Deletion_Peaks"].split("|")
tumorscape_amp_peaks = mut["TUMORScape_Amplification_Peaks"].split("|")
tumorscape_del_peaks = mut["TUMORScape_Deletion_Peaks"].split("|")
full_name = mut["HGNC_Approved Name"]
cosmic = {
"tissue_types_affected": mut["COSMIC_Tissue_tissue_types_affected"],
"total_alterations_in_gene": mut["COSMIC_Tissue_tissue_types_affected"],
}
alt_aliases = list(
itertools.chain([mut["HGNC_Previous Symbols"].split(", "), mut["HGNC_Synonyms"].split(", ")])
)
location = mut["HGNC_Chromosome"]
uniprot_accession = mut["UniProt_uniprot_accession"]
transcripts = mut["transcripts"]
self.assertTrue(transcripts is not None)
self.assertTrue(len(transcripts) > 0)
self.assertTrue(transcripts.startswith("ENST"))
strand = mut["strand"]
klass = mut["class"]
uniprot_experimentals = mut["UniProt_AA_experimental_info"].split("|")
self.assertTrue(uniprot_experimentals is not None)
uniprot_natural_variations = mut["UniProt_AA_natural_variation"].split("|")
uniprot_regions = mut["UniProt_AA_region"].split("|")
uniprot_sites = mut["UniProt_AA_site"].split("|")
uniprot_go_biological_processes = mut["UniProt_GO_Biological_Process"].split("|")
uniprot_go_cellular_components = mut["UniProt_GO_Cellular_Component"].split("|")
self.assertTrue(uniprot_go_cellular_components is not None)
uniprot_go_molecular_functions = mut["UniProt_GO_Molecular_Function"].split("|")
pass
def test_querying_transcripts_by_region(self):
"""Test web api backend call /transcripts/.... """
datasource_list = DatasourceFactory.createDatasources(
self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
txs = annotator.retrieve_transcripts_by_region("4", 50164411, 60164411)
self.assertTranscriptsFound(txs)
## Here is an example of getting enough data to populate the json in doc/transcript_json_commented.json.txt
# None of these values are validated.
for tx in txs:
transcript_id = tx.get_transcript_id()
tx_start = tx.determine_transcript_start()
tx_end = tx.determine_transcript_stop()
gene = tx.get_gene()
chr = tx.get_contig()
n_exons = len(tx.get_exons())
strand = tx.get_strand()
footprint_start, footprint_end = tx.determine_cds_footprint()
klass = tx.get_gene_type()
cds_start = tx.determine_cds_start()
cds_end = tx.determine_cds_stop()
id = tx.get_gene_id()
genomic_coords = [[exon[0], exon[1]] for exon in tx.get_exons()]
transcript_coords = [[
TranscriptProviderUtils.convert_genomic_space_to_exon_space(
exon[0] + 1, exon[1], tx)
] for exon in tx.get_exons()]
code_len = int(cds_end) - int(cds_start) + 1
# If refseq datasources are not available, this will fail.
# Step 2 annotate the transcript, which produces a dummy mutation with the refseq annotations.
dummy_mut = annotator.annotate_transcript(tx)
refseq_mRNA_id = dummy_mut["gencode_xref_refseq_mRNA_id"]
refseq_prot_id = dummy_mut["gencode_xref_refseq_prot_acc"]
# Description is unavailable right now
description = ""
self.assertTrue(refseq_mRNA_id is not None)
self.assertTrue(refseq_prot_id is not None)
self.assertTrue(len(transcript_coords) == n_exons)
def test_simple_genes_by_region_annotation(self):
"""Test web api backend call /genes/ """
# http://www.broadinstitute.org/oncotator/genes/chr22_22112223_22312558/
# Two genes: chr22:22,112,223-22,312,558
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
# Here is what the API would call....
txs = annotator.retrieve_transcripts_by_region("22", 22112223, 22312558)
self.assertTranscriptsFound(txs)
mut_dict = annotator.annotate_genes_given_txs(txs)
# Each mut will be for a separate gene
for gene in mut_dict.keys():
mut = mut_dict[gene]
alt_accessions = mut['UniProt_alt_uniprot_accessions'].split("|")
tcgascape_amp_peaks = mut['TCGAScape_Amplification_Peaks'].split("|")
tcgascape_del_peaks = mut['TCGAScape_Deletion_Peaks'].split("|")
tumorscape_amp_peaks = mut['TUMORScape_Amplification_Peaks'].split("|")
tumorscape_del_peaks = mut['TUMORScape_Deletion_Peaks'].split("|")
full_name = mut['HGNC_Approved Name']
cosmic = {"tissue_types_affected": mut['COSMIC_Tissue_tissue_types_affected'], "total_alterations_in_gene": mut["COSMIC_Tissue_tissue_types_affected"]}
alt_aliases = list(itertools.chain([mut["HGNC_Previous Symbols"].split(", "), mut["HGNC_Synonyms"].split(", ")]))
location = mut["HGNC_Chromosome"]
uniprot_accession = mut["UniProt_uniprot_accession"]
transcripts = mut['transcripts']
self.assertTrue(transcripts is not None)
self.assertTrue(len(transcripts) > 0)
self.assertTrue(transcripts.startswith('ENST'))
strand = mut['strand']
klass = mut['class']
uniprot_experimentals = mut['UniProt_AA_experimental_info'].split("|")
self.assertTrue(uniprot_experimentals is not None)
uniprot_natural_variations = mut['UniProt_AA_natural_variation'].split("|")
uniprot_regions = mut['UniProt_AA_region'].split("|")
uniprot_sites = mut['UniProt_AA_site'].split("|")
uniprot_go_biological_processes = mut["UniProt_GO_Biological_Process"].split("|")
uniprot_go_cellular_components = mut["UniProt_GO_Cellular_Component"].split("|")
self.assertTrue(uniprot_go_cellular_components is not None)
uniprot_go_molecular_functions = mut["UniProt_GO_Molecular_Function"].split("|")
pass
def test_querying_transcripts_by_region(self):
"""Test web api backend call /transcripts/.... """
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
txs = annotator.retrieve_transcripts_by_region("4", 50164411, 60164411)
self.assertTranscriptsFound(txs)
## Here is an example of getting enough data to populate the json in doc/transcript_json_commented.json.txt
# None of these values are validated.
for tx in txs:
transcript_id = tx.get_transcript_id()
tx_start = tx.determine_transcript_start()
tx_end = tx.determine_transcript_stop()
gene = tx.get_gene()
chr = tx.get_contig()
n_exons = len(tx.get_exons())
strand = tx.get_strand()
footprint_start, footprint_end = tx.determine_cds_footprint()
klass = tx.get_gene_type()
cds_start = tx.determine_cds_start()
cds_end = tx.determine_cds_stop()
id = tx.get_gene_id()
genomic_coords = [[exon[0], exon[1]] for exon in tx.get_exons()]
transcript_coords = [
[TranscriptProviderUtils.convert_genomic_space_to_exon_space(exon[0] + 1, exon[1], tx)]
for exon in tx.get_exons()
]
code_len = int(cds_end) - int(cds_start) + 1
# If refseq datasources are not available, this will fail.
# Step 2 annotate the transcript, which produces a dummy mutation with the refseq annotations.
dummy_mut = annotator.annotate_transcript(tx)
refseq_mRNA_id = dummy_mut["gencode_xref_refseq_mRNA_id"]
refseq_prot_id = dummy_mut["gencode_xref_refseq_prot_acc"]
# Description is unavailable right now
description = ""
self.assertTrue(refseq_mRNA_id is not None)
self.assertTrue(refseq_prot_id is not None)
self.assertTrue(len(transcript_coords) == n_exons)
