scout/build/genes/transcript.py
def build_transcript(transcript_info, build='37'):
    """Build a hgnc_transcript object

        Args:
            transcript_info(dict): Transcript information

        Returns:
            transcript_obj(HgncTranscript)
            {
                transcript_id: str, required
                hgnc_id: int, required
                build: str, required
                refseq_id: str,
                chrom: str, required
                start: int, required
                end: int, required
                is_primary: bool
            }
    """
    try:
        transcript_id = transcript_info['ensembl_transcript_id']
    except KeyError:
        raise KeyError("Transcript has to have ensembl id")
    
    build = build
    is_primary = transcript_info.get('is_primary', False)
    
    refseq_id = transcript_info.get('refseq_id')
    refseq_identifiers = transcript_info.get('refseq_identifiers')

    try:
        chrom = transcript_info['chrom']
    except KeyError:
        raise KeyError("Transcript has to have a chromosome")
    
    try:
        start = int(transcript_info['transcript_start'])
    except KeyError:
        raise KeyError("Transcript has to have start")
    except TypeError:
        raise TypeError("Transcript start has to be integer")

    try:
        end = int(transcript_info['transcript_end'])
    except KeyError:
        raise KeyError("Transcript has to have end")
    except TypeError:
        raise TypeError("Transcript end has to be integer")

    try:
        hgnc_id = int(transcript_info['hgnc_id'])
    except KeyError:
        raise KeyError("Transcript has to have a hgnc id")
    except TypeError:
        raise TypeError("hgnc id has to be integer")

    transcript_obj = HgncTranscript(
        transcript_id=transcript_id, 
        hgnc_id=hgnc_id, 
        chrom=chrom, 
        start=start, 
        end=end, 
        is_primary=is_primary, 
        refseq_id=refseq_id,
        refseq_identifiers=refseq_identifiers,
        build=build
    )
    # Remove unnessesary keys
    for key in list(transcript_obj):
        if transcript_obj[key] is None:
            transcript_obj.pop(key)

    return transcript_obj
def build_transcript(transcript_info, build='37'):
    """Build a hgnc_transcript object

        Args:
            transcript_info(dict): Transcript information

        Returns:
            transcript_obj(HgncTranscript)
            {
                transcript_id: str, required
                hgnc_id: int, required
                build: str, required
                refseq_id: str,
                chrom: str, required
                start: int, required
                end: int, required
                is_primary: bool
            }
    """
    try:
        transcript_id = transcript_info['ensembl_transcript_id']
    except KeyError:
        raise KeyError("Transcript has to have ensembl id")
    
    build = build
    is_primary = transcript_info.get('is_primary', False)
    
    refseq_id = transcript_info.get('refseq_id')
    refseq_identifiers = transcript_info.get('refseq_identifiers')

    try:
        chrom = transcript_info['chrom']
    except KeyError:
        raise KeyError("Transcript has to have a chromosome")
    
    try:
        start = int(transcript_info['transcript_start'])
    except KeyError:
        raise KeyError("Transcript has to have start")
    except TypeError:
        raise TypeError("Transcript start has to be integer")

    try:
        end = int(transcript_info['transcript_end'])
    except KeyError:
        raise KeyError("Transcript has to have end")
    except TypeError:
        raise TypeError("Transcript end has to be integer")

    try:
        hgnc_id = int(transcript_info['hgnc_id'])
    except KeyError:
        raise KeyError("Transcript has to have a hgnc id")
    except TypeError:
        raise TypeError("hgnc id has to be integer")

    transcript_obj = HgncTranscript(
        transcript_id=transcript_id, 
        hgnc_id=hgnc_id, 
        chrom=chrom, 
        start=start, 
        end=end, 
        is_primary=is_primary, 
        refseq_id=refseq_id,
        refseq_identifiers=refseq_identifiers,
        build=build
    )
    # Remove unnessesary keys
    for key in list(transcript_obj):
        if transcript_obj[key] is None:
            transcript_obj.pop(key)

    return transcript_obj
Build a hgnc_transcript object

        Args:
            transcript_info(dict): Transcript information

        Returns:
            transcript_obj(HgncTranscript)
            {
                transcript_id: str, required
                hgnc_id: int, required
                build: str, required
                refseq_id: str,
                chrom: str, required
                start: int, required
                end: int, required
                is_primary: bool
            }