def _get_gene_detailed(self):
"""
define a gene detailed table
"""
#unique identifier for each entry
i = 0
table_contents = detailed_list = []
config = read_gemini_config(args=self.args)
path_dirname = config["annotation_dir"]
file_handle = os.path.join(path_dirname, 'detailed_gene_table_v75')
for line in open(file_handle, 'r'):
field = line.strip().split("\t")
if not field[0].startswith("Chromosome"):
i += 1
table = gene_table.gene_detailed(field)
detailed_list = [
str(i), table.chrom, table.gene, table.is_hgnc,
table.ensembl_gene_id, table.ensembl_trans_id,
table.biotype, table.trans_status, table.ccds_id,
table.hgnc_id, table.entrez, table.cds_length,
table.protein_length, table.transcript_start,
table.transcript_end, table.strand, table.synonym,
table.rvis, table.mam_phenotype
]
table_contents.append(detailed_list)
database.insert_gene_detailed(self.c, table_contents)
def _get_gene_detailed(self):
"""
define a gene detailed table
"""
#unique identifier for each entry
i = 0
table_contents = detailed_list = []
config = read_gemini_config(args=self.args)
path_dirname = config["annotation_dir"]
file_handle = os.path.join(path_dirname, 'detailed_gene_table_v75')
for line in open(file_handle, 'r'):
field = line.strip().split("\t")
if not field[0].startswith("Chromosome"):
i += 1
table = gene_table.gene_detailed(field)
detailed_list = [str(i),table.chrom,table.gene,table.is_hgnc,
table.ensembl_gene_id,table.ensembl_trans_id,
table.biotype,table.trans_status,table.ccds_id,
table.hgnc_id,table.entrez,table.cds_length,table.protein_length,
table.transcript_start,table.transcript_end,
table.strand,table.synonym,table.rvis,table.mam_phenotype]
table_contents.append(detailed_list)
database.insert_gene_detailed(self.c, table_contents)