本文整理汇总了Python中oncotator.Annotator.Annotator.annotate_transcript方法的典型用法代码示例。如果您正苦于以下问题：Python Annotator.annotate_transcript方法的具体用法？Python Annotator.annotate_transcript怎么用？Python Annotator.annotate_transcript使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类oncotator.Annotator.Annotator的用法示例。
在下文中一共展示了Annotator.annotate_transcript方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_querying_transcripts_by_region
# 需要导入模块: from oncotator.Annotator import Annotator [as 别名]
# 或者: from oncotator.Annotator.Annotator import annotate_transcript [as 别名]
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)