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
def build_transcript ( transcript , build = '37' ) : # 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)
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 )