def import_genes(filename, chromosome, genome, verbose = False):
from gene_crawler import crawl_genes
from tridentdb.models import Genes, Genome
from django.db.utils import DatabaseError
if not chromosome:
raise Exception("Missing Chromosome information")
if not genome:
raise Exception("Missing Genome information")
genome = Genome.objects.filter(genome_ver = genome)
if len(genome) != 1:
raise ImportException("Genome, '{0}', has not yet been loaded into the database.".format(genome))
genes = crawl_genes(filename)
genome = genome[0]
for gene in genes:
if verbose:
print("Importing {0}".format(gene.name))
(start, end) = gene.get_coords()
dbentry = Genes(name = gene.name, genomic_start = start, genomic_end = end,synonyms = gene.synonym, is_on_positive_strand = (gene.direction == "+"), chromosome = chromosome, db_xref = ",".join(gene.db_xref), genome_id = genome.id)
try:
dbentry.save()
except DatabaseError as de:
from sys import stderr
from gene_crawler import write_gene
stderr.write("Error loading gene:")
write_gene(gene, stderr)
raise de
def test_gene_indexer():
from gene_crawler import crawl_genes, write_gene
import StringIO as SIO
from os.path import join
canonical = open(join("test", "indexer.out.expected"), "r")
genes = crawl_genes(join("test", "test.gbs"))
buf = SIO.StringIO()
for gene in genes:
write_gene(gene, buf)
buf.seek(0)
if buf.read() == canonical.read():
print("Gene Indexer test passed")
return
buf.seek(0)
canonical.seek(0)
print("Expected:")
print(canonical.read())
print("Produced:")
print(buf.read())
raise Exception("Gene Indexter test failed")
def import_genes(filename, chromosome, genome, verbose=False):
from gene_crawler import crawl_genes
from tridentdb.models import Genes, Genome
from django.db.utils import DatabaseError
if not chromosome:
raise Exception("Missing Chromosome information")
if not genome:
raise Exception("Missing Genome information")
genome = Genome.objects.filter(genome_ver=genome)
if len(genome) != 1:
raise ImportException(
"Genome, '{0}', has not yet been loaded into the database.".format(
genome))
genes = crawl_genes(filename)
genome = genome[0]
for gene in genes:
if verbose:
print("Importing {0}".format(gene.name))
(start, end) = gene.get_coords()
dbentry = Genes(name=gene.name,
genomic_start=start,
genomic_end=end,
synonyms=gene.synonym,
is_on_positive_strand=(gene.direction == "+"),
chromosome=chromosome,
db_xref=",".join(gene.db_xref),
genome_id=genome.id)
try:
dbentry.save()
except DatabaseError as de:
from sys import stderr
from gene_crawler import write_gene
stderr.write("Error loading gene:")
write_gene(gene, stderr)
raise de
