gene_table.py

import os
import database
from gemini.config import read_gemini_config

class gene_custom_map:
    def __init__(self,gene):
        gen = [None if g == 'None' else g for g in gene]

        self.chrom = gen[0]
        self.transcript_min_start = gen[1]
        self.transcript_max_end = gen[2]
        self.gene = gen[3]

    def __str__(self):
        return ",".join([self.chrom, self.transcript_min_start,self.transcript_max_end,self.gene])


class gene_detailed:

    def __init__(self, field):
        field = [None if f == 'None' else f for f in field]
        self.fields = field[:]
        self.chrom = field[0]
        self.gene = field[1]
        self.is_hgnc = field[2]
        self.ensembl_gene_id = field[3]
        self.ensembl_trans_id = field[4]
        self.biotype = field[5]
        self.trans_status = field[6]
        self.ccds_id = field[7]
        self.hgnc_id = field[8]
        self.cds_length = field[9]
        self.protein_length = field[10]
        self.transcript_start = field[11]
        self.transcript_end = field[12]
        self.strand = field[13]
        self.synonym = field[14]
        self.rvis = field[15]
        self.entrez = field[16]
        self.mam_phenotype = field[17]

    def __str__(self):
        return ",".join([self.chrom, self.gene, self.is_hgnc, self.ensembl_gene_id, self.ensembl_trans_id, self.biotype, self.trans_status,
                         self.ccds_id, self.hgnc_id, self.cds_length, self.protein_length, self.transcript_start, self.transcript_end, self.strand,
                         str(self.synonym), self.rvis, self.entrez, self.mam_phenotype])

class gene_summary:

    def __init__(self, col):
         col = [None if f == 'None' else f for f in col]
         self.columns = col[:]
         self.chrom = col[0]
         self.gene = col[1]
         self.is_hgnc = col[2]
         self.ensembl_gene_id = col[3]
         self.hgnc_id = col[4]
         self.synonym = col[5]
         self.rvis = col[6]
         self.strand = col[7]
         self.transcript_min_start = col[8]
         self.transcript_max_end = col[9]
         self.mam_phenotype = col[10]

    def __str__(self):
        return ",".join([self.chrom, self.gene, self.is_hgnc, self.ensembl_gene_id, self.hgnc_id, self.synonym, self.rvis,
                         self.strand, self.transcript_min_start, self.transcript_max_end, self.mam_phenotype])

def update_cosmic_census_genes(session, metadata, args):
    """
    Update the gene summary table with
    whether or not a given gene is in the
    COSMIC cancer gene census
    """
    config = read_gemini_config(args=args)
    path_dirname = config["annotation_dir"]
    file = os.path.join(path_dirname, 'cancer_gene_census.20140120.tsv')

    cosmic_census_genes = []
    for line in open(file, 'r'):
        fields = line.strip().split("\t")
        gene = fields[0]
        chrom = "chr" + fields[3]
        cosmic_census_genes.append((1, gene, chrom))

    database.update_gene_summary_w_cancer_census(session, metadata, cosmic_census_genes)