Python TranscriptProviderUtils.determine_exon_index方法代码示例

# 需要导入模块: from oncotator.TranscriptProviderUtils import TranscriptProviderUtils [as 别名]
# 或者: from oncotator.TranscriptProviderUtils.TranscriptProviderUtils import determine_exon_index [as 别名]
    def _determine_vc_for_cds_overlap(self, start, end, ref_allele, alt_allele, is_frameshift_indel, is_splice_site, tx, variant_type, is_start_codon):
        """
        Note: This method can also handle start and stop codons.

        :param start:
        :param end:
        :param ref_allele:
        :param alt_allele:
        :param is_frameshift_indel:
        :param is_splice_site:
        :param tx:
        :param variant_type:
        :return:
        """
        observed_allele_stranded, reference_allele_stranded = self._get_stranded_alleles(ref_allele, alt_allele, tx)
        transcript_position_start, transcript_position_end = TranscriptProviderUtils.convert_genomic_space_to_exon_space(
            start, end, tx)

        if tx.get_strand() == "+" and not variant_type == VariantClassification.VT_INS:
            transcript_position_start -= 1
            transcript_position_end -= 1

        transcript_seq = tx.get_seq()
        protein_seq = tx.get_protein_seq()
        cds_start, cds_stop = TranscriptProviderUtils.determine_cds_in_exon_space(tx)
        protein_position_start, protein_position_end = TranscriptProviderUtils.get_protein_positions(
            transcript_position_start,
            transcript_position_end, cds_start)
        new_ref_transcript_seq = transcript_seq
        if (transcript_seq[transcript_position_start:transcript_position_end+1] != reference_allele_stranded) and variant_type != VariantClassification.VT_INS:
            new_ref_transcript_seq = list(transcript_seq)
            new_ref_transcript_seq[transcript_position_start:transcript_position_end+1] = reference_allele_stranded
            new_ref_transcript_seq = ''.join(new_ref_transcript_seq)
            ref_tx_seq_has_been_changed = True
        else:
            ref_tx_seq_has_been_changed = False
        cds_codon_start, cds_codon_end = TranscriptProviderUtils.get_cds_codon_positions(protein_position_start, protein_position_end, cds_start)

        if variant_type == "DEL":
            reference_codon_seq = new_ref_transcript_seq[cds_codon_start:cds_codon_end+1].lower()
        else:
            reference_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(new_ref_transcript_seq[cds_codon_start:cds_codon_end+1].lower(), cds_codon_start, transcript_position_start, transcript_position_end, reference_allele_stranded, variant_type)

        if variant_type == "INS" and tx.get_strand() == "-":
            mutated_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(reference_codon_seq.lower(), cds_codon_start - 1, transcript_position_start, transcript_position_end, observed_allele_stranded, variant_type)
        else:
            mutated_codon_seq = TranscriptProviderUtils.mutate_reference_sequence(reference_codon_seq.lower(), cds_codon_start, transcript_position_start, transcript_position_end, observed_allele_stranded, variant_type)


        observed_aa = Bio.Seq.translate(mutated_codon_seq)
        if ref_tx_seq_has_been_changed:
            reference_aa = Bio.Seq.translate(reference_codon_seq)
        else:
            reference_aa = protein_seq[protein_position_start-1:protein_position_end]

        if variant_type != VariantClassification.VT_SNP:

            try:
                reference_aa, observed_aa, protein_position_start, protein_position_end = \
                    self._adjust_protein_position_and_alleles(protein_seq, protein_position_start,
                        protein_position_end, reference_aa, observed_aa)
            except InvalidVariantException as ive:
                logging.getLogger(__name__).error("Could not properly adjust protein position for variant: %s, %s, %s, %s, %s VT: %s" % (tx.get_contig(), start, end, ref_allele, alt_allele, variant_type))
                logging.getLogger(__name__).error(str(ive))
                logging.getLogger(__name__).warn("Above error may not have exact start and end positions if this is a VCF input.")
                logging.getLogger(__name__).warn("Variant type is likely incorrect.  This can happen with some GATK VCFs")
                logging.getLogger(__name__).warn(TranscriptProviderUtils.is_valid_xNP(variant_type, ref_allele, alt_allele))
                logging.getLogger(__name__).warn("The protein_change annotation may not be properly rendered.")

        vc_tmp, vc_tmp_secondary = self.infer_variant_classification(variant_type, reference_aa, observed_aa, ref_allele, alt_allele,
                                                   is_frameshift_indel=is_frameshift_indel, is_splice_site=is_splice_site, is_start_codon=is_start_codon)

        cds_start_exon_space, cds_end_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(tx)
        exon_i = TranscriptProviderUtils.determine_exon_index(int(start), int(end), tx, variant_type)
        final_vc = VariantClassification(vc_tmp, variant_type, transcript_id=tx.get_transcript_id(), alt_codon=mutated_codon_seq, ref_codon=reference_codon_seq, ref_aa=reference_aa, ref_protein_start=protein_position_start, ref_protein_end=protein_position_end, alt_aa=observed_aa, alt_codon_start_in_exon=cds_codon_start, alt_codon_end_in_exon=cds_codon_end, ref_codon_start_in_exon=cds_codon_start, ref_codon_end_in_exon=cds_codon_end, cds_start_in_exon_space=cds_start_exon_space, ref_allele_stranded=reference_allele_stranded, alt_allele_stranded=observed_allele_stranded, exon_i=exon_i, vc_secondary=vc_tmp_secondary)
        return final_vc