Python TranscriptProviderUtils.determine_cds_in_exon_space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_cds_in_exon_space [as 别名]
    def _determine_de_novo(self, vc_str, exon_start, ref, alt, tx, variant_type, buffer=2 ):
        """Returns input vc if not de Novo.  Otherwise, returns updated variant classification.

        :param exon_start:
        :param buffer:
        :param vc_str: Current variant classification.  Note that if this is not 5'UTR, this method will just return this input.
        :param ref: (str) Does not take into account strandedness (e.g. m.ref_allele)
        :param alt: (str) Does not take into account strandedness (e.g. m.alt_allele)
        :param tx: transcript
        :param variant_type:
         Will always return original vc if the vc is not None."""
        result = vc_str
        if vc_str == VariantClassification.FIVE_PRIME_UTR and ref != alt:
            mutated_utr_region = self._mutate_exon(tx, ref, alt, variant_type, exon_start, buffer)
            atg_position = mutated_utr_region.find('ATG')
            if atg_position > -1:
                atg_exon_position = exon_start + atg_position - buffer
                cds_start_in_exon_space, cds_end_in_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(tx)
                if (cds_start_in_exon_space - atg_exon_position) % 3 == 0:
                    frameness = 'InFrame'
                else:
                    frameness = 'OutOfFrame'
                result = 'De_novo_Start_' + frameness

        return result

# 需要导入模块: from oncotator.TranscriptProviderUtils import TranscriptProviderUtils [as 别名]
# 或者: from oncotator.TranscriptProviderUtils.TranscriptProviderUtils import determine_cds_in_exon_space [as 别名]
    def test_codon_single_base(self, start, end, ref_base_stranded, gt_codon):
        """Test that we can grab the proper three bases of a codon for an arbitrary single base """
        tx = self.retrieve_test_transcript_MAPK1()
        transcript_position_start, transcript_position_end = TranscriptProviderUtils.convert_genomic_space_to_exon_space(start, end, tx)
        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)
        cds_codon_start, cds_codon_end = TranscriptProviderUtils.get_cds_codon_positions(protein_position_start, protein_position_end, cds_start)

        codon_seq = tx.get_seq()[cds_codon_start:cds_codon_end+1]
        self.assertTrue(codon_seq == gt_codon, "Did not get correct codon (%s): %s    loc: %s-%s" %(gt_codon, codon_seq, start, end))

# 需要导入模块: from oncotator.TranscriptProviderUtils import TranscriptProviderUtils [as 别名]
# 或者: from oncotator.TranscriptProviderUtils.TranscriptProviderUtils import determine_cds_in_exon_space [as 别名]
    def _determine_de_novo_old(self, vc, transcript_position_start, transcript_position_end, ref, alt, tx, variant_type):
        """Returns input vc if not de Novo.  Otherwise, returns updated variant classification.

        :param vc: Current variant classification.  Note that if this is not 5'UTR, this method will just return this input.
        :param transcript_position_start:
        :param transcript_position_end:
        :param ref: (str) Does not take into account strandedness (e.g. m.ref_allele)
        :param alt: (str) Does not take into account strandedness (e.g. m.alt_allele)
        :param tx: transcript
        :param variant_type:
         Will always return original vc if the vc is not None."""
        result = vc

        if vc == VariantClassification.FIVE_PRIME_UTR and ref != alt:
            observed_allele_stranded = self._determine_stranded_allele(alt, tx.get_strand())
            reference_allele_stranded = self._determine_stranded_allele(ref, tx.get_strand())
            tx_seq = tx.get_seq()

            if variant_type == VariantClassification.VT_INS:
                if tx.get_strand() == "-":
                    transcript_position_start = transcript_position_end
                else:
                    transcript_position_end = transcript_position_start
            utr_region_start, utr_region_end = transcript_position_start-2, transcript_position_end+2
            # TODO: This may not work for "+" strand.  Need unit test.
            utr_region_seq = tx_seq[utr_region_start:utr_region_end+1]

            mutated_utr_region_seq = TranscriptProviderUtils.mutate_reference_sequence(utr_region_seq, utr_region_start,
                transcript_position_start, transcript_position_end, observed_allele_stranded, variant_type)
            # Check for Denovo
            ATG_position = mutated_utr_region_seq.find('ATG')
            if ATG_position > -1:
                cds_start_in_exon_space, cds_end_in_exon_space = TranscriptProviderUtils.determine_cds_in_exon_space(tx)

                ATG_position = utr_region_start + ATG_position + 1
                if (cds_start_in_exon_space - ATG_position) % 3 == 0:
                    frameness = 'InFrame'
                else:
                    frameness = 'OutOfFrame'
                result = 'De_novo_Start_' + frameness
        return result

# 需要导入模块: from oncotator.TranscriptProviderUtils import TranscriptProviderUtils [as 别名]
# 或者: from oncotator.TranscriptProviderUtils.TranscriptProviderUtils import determine_cds_in_exon_space [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