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
def build_transcript ( transcript_info , build = '37' ) : 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
            }
Build a hgnc_transcript object