本文整理汇总了Python中oncotator.TranscriptProviderUtils.TranscriptProviderUtils.determine_closest_exon方法的典型用法代码示例。如果您正苦于以下问题：Python TranscriptProviderUtils.determine_closest_exon方法的具体用法？Python TranscriptProviderUtils.determine_closest_exon怎么用？Python TranscriptProviderUtils.determine_closest_exon使用的例子？那么, 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.TranscriptProviderUtils.TranscriptProviderUtils的用法示例。
在下文中一共展示了TranscriptProviderUtils.determine_closest_exon方法的2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: _extract_exon_info
# 需要导入模块: from oncotator.TranscriptProviderUtils import TranscriptProviderUtils [as 别名]
# 或者: from oncotator.TranscriptProviderUtils.TranscriptProviderUtils import determine_closest_exon [as 别名]
def _extract_exon_info(self, position, tx):
"""
Create basic information about the given position relative to the transcript.
:param int position: in genomic space
:param Transcript tx:
:return tuple:
[0]: closest exon index of the position (0-based),
[1]: whether the distance was left in genomic space (false for overlap)
[2]: whether the position overlaps an exon
"""
exon_index = TranscriptProviderUtils.determine_closest_exon(tx, position, position)
if exon_index is None:
return exon_index, None, None, None
left_distance, right_distance = TranscriptProviderUtils.determine_closest_distance_from_exon(position, position,
exon_index, tx)
is_in_exon = (left_distance <= 0) and (right_distance >= 0)
is_diff_is_positive = (left_distance > 0) and (right_distance > 0)
is_negative_strand = (tx.get_strand() == "-")
return exon_index, is_diff_is_positive, is_in_exon, is_negative_strand示例2: variant_classify
# 需要导入模块: from oncotator.TranscriptProviderUtils import TranscriptProviderUtils [as 别名]
# 或者: from oncotator.TranscriptProviderUtils.TranscriptProviderUtils import determine_closest_exon [as 别名]
def variant_classify(self, tx, ref_allele, alt_allele, start, end, variant_type, dist=2):
"""Perform classifications.
Everything handled in genomic space
*RNA*
x'UTR
Splice_Site (Intron)
Intron
Splice_Site (Exon)
{Missense, Silent}
{Nonsense, Silent}
{Nonstop, Silent}
IGR
x'Flank
De_novo_Start
"""
gene_type = tx.get_gene_type()
if gene_type != "protein_coding":
if gene_type == VariantClassification.LINCRNA:
return VariantClassification(VariantClassification.LINCRNA, variant_type, tx.get_transcript_id())
else:
return VariantClassification(VariantClassification.RNA, variant_type, tx.get_transcript_id())
if ref_allele == "-":
ref_allele = ""
if alt_allele == "-":
alt_allele = ""
s = int(start)
e = int(end)
is_exon_overlap = TranscriptProviderUtils.determine_if_exon_overlap(s, e, tx, variant_type)
is_splice_site_tuple = self._determine_if_splice_site_overlap(s, e, tx, variant_type, dist)
is_splice_site = is_splice_site_tuple[0]
is_beyond_exons, side, is_flank = self._determine_beyond_exon_info_vt(start, end, tx, variant_type)
if not is_exon_overlap and not is_beyond_exons:
exon_i = TranscriptProviderUtils.determine_closest_exon(tx, int(start), int(end))
if is_splice_site:
# Intron Splice Site
return VariantClassification(VariantClassification.SPLICE_SITE, variant_type, tx.get_transcript_id(), vc_secondary=VariantClassification.INTRON, exon_i=exon_i)
else:
return VariantClassification(VariantClassification.INTRON, variant_type, tx.get_transcript_id(), exon_i=exon_i)
if not is_exon_overlap and is_beyond_exons:
if is_flank:
# Flanks
if side.startswith("3"):
return VariantClassification(VariantClassification.THREE_PRIME_PRIME_FLANK, variant_type, transcript_id=tx.get_transcript_id())
else:
return VariantClassification(VariantClassification.FIVE_PRIME_PRIME_FLANK, variant_type, transcript_id=tx.get_transcript_id())
else:
# IGR
return VariantClassification(VariantClassification.IGR, variant_type)
is_start_codon_overlap = self._determine_codon_overlap(s, e, tx.get_start_codon(), variant_type)
is_stop_codon_overlap = self._determine_codon_overlap(s, e, tx.get_stop_codon(), variant_type)
if is_start_codon_overlap and not variant_type.endswith("NP"):
return VariantClassification('Start_Codon_' + variant_type.capitalize(), variant_type, transcript_id=tx.get_transcript_id())
if is_stop_codon_overlap and not variant_type.endswith("NP"):
return VariantClassification('Stop_Codon_' + variant_type.capitalize(), variant_type, transcript_id=tx.get_transcript_id())
is_cds_overlap = self._determine_if_cds_overlap(s, e, tx, variant_type)
if is_exon_overlap and not is_cds_overlap and not is_start_codon_overlap and not is_stop_codon_overlap:
# UTR
if side.startswith("3"):
vc_tmp = VariantClassification.THREE_PRIME_UTR
else:
vc_tmp = VariantClassification.FIVE_PRIME_UTR
transcript_position_exon_space_start, transcript_position_exon_space_end = TranscriptProviderUtils.convert_genomic_space_to_exon_space(start, end, tx)
vc = self._determine_de_novo(vc_tmp, transcript_position_exon_space_start, ref_allele, alt_allele, tx, variant_type)
return VariantClassification(vc, variant_type, transcript_id=tx.get_transcript_id(), )
# We have a clean overlap in the CDS. Includes start codon or stop codon.
if is_cds_overlap or is_stop_codon_overlap or is_start_codon_overlap:
is_frameshift_indel = self.is_frameshift_indel(variant_type, int(start), int(end), alt_allele)
return self._determine_vc_for_cds_overlap(start, end, ref_allele, alt_allele, is_frameshift_indel, is_splice_site, tx, variant_type, is_start_codon_overlap)
raise ValueError("Could not determine variant classification: " + tx.get_trancript_id() + " " + str([ref_allele, alt_allele, start, end]))