How to use the pyensembl.transcript.Transcript function in pyensembl

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github openvax / pyensembl / pyensembl / transcript.py View on Github external
def __eq__(self, other):
        return (
            other.__class__ is Transcript and
            self.id == other.id and
            self.genome == other.genome)
github openvax / pyensembl / pyensembl / genome.py View on Github external
if len(result) < 5 or len(result) > (5 + len(optional_field_names)):
                raise ValueError(
                    "Result is not the expected length: %d" % len(result))
            contig, start, end, strand, gene_id = result[:5]
            if len(result) > 5:
                extra_field_names = [f for f in optional_field_names if f in field_names]
                extra_data = dict(zip(extra_field_names, result[5:]))
                transcript_name = extra_data.get("transcript_name")
                transcript_biotype = extra_data.get("transcript_biotype")
                tsl = extra_data.get("transcript_support_level")
                if not tsl or tsl == 'NA':
                    tsl = None
                else:
                    tsl = int(tsl)

            self._transcripts[transcript_id] = Transcript(
                transcript_id=transcript_id,
                transcript_name=transcript_name,
                contig=contig,
                start=start,
                end=end,
                strand=strand,
                biotype=transcript_biotype,
                gene_id=gene_id,
                genome=self,
                support_level=tsl)

        return self._transcripts[transcript_id]
github openvax / varcode / varcode / core_logic.py View on Github external
Parameters
    ----------
    variant : Variant
        Genomic variant

    transcript :  Transcript
        Transcript we're going to mutate
    """

    if not isinstance(variant, Variant):
        raise TypeError(
            "Expected %s : %s to have type Variant" % (
                variant, type(variant)))

    if not isinstance(transcript, Transcript):
        raise TypeError(
            "Expected %s : %s to have type Transcript" % (
                transcript, type(transcript)))

    # check for non-coding transcripts first, since
    # every non-coding transcript is "incomplete".
    if not is_coding_biotype(transcript.biotype):
        return NoncodingTranscript(variant, transcript)

    if not transcript.complete:
        return IncompleteTranscript(variant, transcript)

    if not overlaps_any_exon(variant, transcript):
        return Intronic(variant, transcript)

    return infer_exonic_effect(variant, transcript)