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)
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()
path_dirname = config["annotation_dir"]
file_handle = os.path.join(path_dirname, 'detailed_gene_table_v75')
header= ['uid','chrom','gene','is_hgnc','ensembl_gene_id','transcript','biotype','transcript_status','ccds_id','hgnc_id',\
'entrez_id','cds_length','protein_length','transcript_start','transcript_end','strand','synonym','rvis_pct','mam_phenotype_id']
import csv
with open('../gene_detailed.csv', 'wb') as csvfile:
rowwriter = csv.writer(csvfile, delimiter=',',
quotechar='|', quoting=csv.QUOTE_MINIMAL)
rowwriter.writerow(header)
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]
rowwriter.writerow(detailed_list)
# if(i==5):
# print detailed_list
# table_contents.append(detailed_list)
#database.insert_gene_detailed(self.c, table_contents)
"""