TCGA_MAF.py

class TCGA_MAF(object):
    fields=["Hugo_Symbol","Entrez_Gene_Id","Center","NCBI_Build",
            "Chromosome","Start_Position","End_Position","Strand",
            "Variant_Classification","Variant_Type","Reference_Allele",
            "Tumor_Seq_Allele1","Tumor_Seq_Allele2","dbSNP_RS","dbSNP_Val_Status",
            "Tumor_Sample_Barcode","Matched_Norm_Sample_Barcode",
            "Match_Norm_Seq_Allele1","Match_Norm_Seq_Allele2",
            "Tumor_Validation_Allele1","Tumor_Validation_Allele2",
            "Match_Norm_Validation_Allele1","Match_Norm_Validation_Allele2",
            "Verification_Status","Validation_Status","Mutation_Status",
            "Sequencing_Phase","Sequence_Source","Validation_Method",
            "Score","BAM_File","Sequencer",
            "Tumor_Sample_UUID","Matched_Norm_Sample_UUID",
            "t_ref_count", "t_alt_count", "n_ref_count", "n_alt_count", "Caller"]
    @classmethod
    def header(cls):
        return "\t".join(cls.fields)
    @classmethod
    def addFields(cls,newFields):
        cls.fields.extend(newFields)
    def __init__(self, **kw):
        for fi in TCGA_MAF.fields:
            self.__dict__[fi]=""
        self.Center="bic.mskcc.org"
        self.NCBI_Build="hg19"
        for ki in kw:
            self.__dict__[ki]=kw[ki]
    def __str__(self):
        return "\t".join([str(self.__dict__[fi]) for fi in TCGA_MAF.fields])