scout/build/variant/transcript.py
def build_transcript(transcript, build='37'):
    """Build a transcript object
    
    These represents the transcripts that are parsed from the VCF, not
    the transcript definitions that are collected from ensembl.
    
        Args:
            transcript(dict): Parsed transcript information
    
        Returns:
            transcript_obj(dict)
    """
    
    # Transcripts has to have an id
    transcript_id = transcript['transcript_id']
    transcript_obj = dict(
        transcript_id = transcript_id
    )
    
    # Transcripts has to belong to a gene
    transcript_obj['hgnc_id'] = transcript['hgnc_id']

    if transcript.get('protein_id'):
        transcript_obj['protein_id'] = transcript['protein_id']
    
    if transcript.get('sift_prediction'):
        transcript_obj['sift_prediction'] = transcript['sift_prediction']
    
    if transcript.get('polyphen_prediction'):
        transcript_obj['polyphen_prediction'] = transcript['polyphen_prediction']


    if transcript.get('swiss_prot'):
        transcript_obj['swiss_prot'] = transcript['swiss_prot']
    
    if transcript.get('pfam_domain'):
        transcript_obj['pfam_domain'] = transcript.get('pfam_domain')
    
    if transcript.get('prosite_profile'):
        transcript_obj['prosite_profile'] = transcript.get('prosite_profile')
    
    if transcript.get('smart_domain'):
        transcript_obj['smart_domain'] = transcript.get('smart_domain')

    if transcript.get('biotype'):
        transcript_obj['biotype'] = transcript.get('biotype')

    if transcript.get('functional_annotations'):
        transcript_obj['functional_annotations'] = transcript['functional_annotations']
    
    if transcript.get('region_annotations'):
        transcript_obj['region_annotations'] = transcript['region_annotations']

    if transcript.get('exon'):
        transcript_obj['exon'] = transcript.get('exon')
    
    if transcript.get('intron'):
        transcript_obj['intron'] = transcript.get('intron')
    
    if transcript.get('strand'):
        transcript_obj['strand'] = transcript.get('strand')

    if transcript.get('coding_sequence_name'):
        transcript_obj['coding_sequence_name'] = transcript['coding_sequence_name']
    
    if transcript.get('protein_sequence_name'):
        transcript_obj['protein_sequence_name'] = transcript['protein_sequence_name']

    transcript_obj['is_canonical'] = transcript.get('is_canonical', False)

    return transcript_obj
def build_transcript(transcript, build='37'):
    """Build a transcript object
    
    These represents the transcripts that are parsed from the VCF, not
    the transcript definitions that are collected from ensembl.
    
        Args:
            transcript(dict): Parsed transcript information
    
        Returns:
            transcript_obj(dict)
    """
    
    # Transcripts has to have an id
    transcript_id = transcript['transcript_id']
    transcript_obj = dict(
        transcript_id = transcript_id
    )
    
    # Transcripts has to belong to a gene
    transcript_obj['hgnc_id'] = transcript['hgnc_id']

    if transcript.get('protein_id'):
        transcript_obj['protein_id'] = transcript['protein_id']
    
    if transcript.get('sift_prediction'):
        transcript_obj['sift_prediction'] = transcript['sift_prediction']
    
    if transcript.get('polyphen_prediction'):
        transcript_obj['polyphen_prediction'] = transcript['polyphen_prediction']


    if transcript.get('swiss_prot'):
        transcript_obj['swiss_prot'] = transcript['swiss_prot']
    
    if transcript.get('pfam_domain'):
        transcript_obj['pfam_domain'] = transcript.get('pfam_domain')
    
    if transcript.get('prosite_profile'):
        transcript_obj['prosite_profile'] = transcript.get('prosite_profile')
    
    if transcript.get('smart_domain'):
        transcript_obj['smart_domain'] = transcript.get('smart_domain')

    if transcript.get('biotype'):
        transcript_obj['biotype'] = transcript.get('biotype')

    if transcript.get('functional_annotations'):
        transcript_obj['functional_annotations'] = transcript['functional_annotations']
    
    if transcript.get('region_annotations'):
        transcript_obj['region_annotations'] = transcript['region_annotations']

    if transcript.get('exon'):
        transcript_obj['exon'] = transcript.get('exon')
    
    if transcript.get('intron'):
        transcript_obj['intron'] = transcript.get('intron')
    
    if transcript.get('strand'):
        transcript_obj['strand'] = transcript.get('strand')

    if transcript.get('coding_sequence_name'):
        transcript_obj['coding_sequence_name'] = transcript['coding_sequence_name']
    
    if transcript.get('protein_sequence_name'):
        transcript_obj['protein_sequence_name'] = transcript['protein_sequence_name']

    transcript_obj['is_canonical'] = transcript.get('is_canonical', False)

    return transcript_obj
Build a transcript object
    
    These represents the transcripts that are parsed from the VCF, not
    the transcript definitions that are collected from ensembl.
    
        Args:
            transcript(dict): Parsed transcript information
    
        Returns:
            transcript_obj(dict)