def _get_gene_summary(self):
"""
define a gene summary table
"""
#unique identifier for each entry
i = 0
contents = summary_list = []
config = read_gemini_config(args=self.args)
path_dirname = config["annotation_dir"]
file = os.path.join(path_dirname, 'summary_gene_table_v75')
for line in open(file, 'r'):
col = line.strip().split("\t")
if not col[0].startswith("Chromosome"):
i += 1
table = gene_table.gene_summary(col)
# defaul cosmic census to False
cosmic_census = 0
summary_list = [
str(i), table.chrom, table.gene, table.is_hgnc,
table.ensembl_gene_id, table.hgnc_id,
table.transcript_min_start, table.transcript_max_end,
table.strand, table.synonym, table.rvis,
table.mam_phenotype, cosmic_census
]
contents.append(summary_list)
database.insert_gene_summary(self.c, contents)
def _get_gene_summary(self):
"""
define a gene summary table
"""
#unique identifier for each entry
i = 0
contents = summary_list = []
config = read_gemini_config(args=self.args)
path_dirname = config["annotation_dir"]
file = os.path.join(path_dirname, 'summary_gene_table_v75')
for line in open(file, 'r'):
col = line.strip().split("\t")
if not col[0].startswith("Chromosome"):
i += 1
table = gene_table.gene_summary(col)
# defaul cosmic census to False
cosmic_census = 0
summary_list = [str(i),table.chrom,table.gene,table.is_hgnc,
table.ensembl_gene_id,table.hgnc_id,
table.transcript_min_start,
table.transcript_max_end,table.strand,
table.synonym,table.rvis,table.mam_phenotype,
cosmic_census]
contents.append(summary_list)
database.insert_gene_summary(self.c, contents)