def main():
no_threads = 1
db_name = "exolocator_db"
db = connect_to_mysql(user="******", passwd="tooiram")
cursor = db.cursor()
switch_to_db (cursor, db_name)
cfg = ConfigurationReader(user="******", passwd="tooiram", check=False)
# afs is killing me here ...
in_path = cfg.get_path('afs_dumps')+"/exons"
if (not os.path.exists(in_path)):
print in_path, "not found"
cursor.close()
db .close()
###############
os.chdir(in_path)
filenames = glob.glob("*exon_dump.txt")
parallelize (no_threads, load_from_infiles, filenames, in_path)
def main():
no_threads = 1
db = connect_to_mysql()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
parallelize (no_threads, dump_orthos, all_species, [local_db, ensembl_db_name])
def main():
special = 'test'
no_threads = 10
method = 'usearch'
if len(sys.argv) > 1 and len(sys.argv) < 4:
print("usage: %s <set name> <number of threads> <method>" %
sys.argv[0])
exit(1)
elif len(sys.argv) == 4:
special = sys.argv[1]
special = special.lower()
if special == 'none': special = None
no_threads = int(sys.argv[2])
method = sys.argv[3]
if not (method == 'usearch' or method == 'sw_sharp'):
print("unrecognized method: ", method)
exit(1)
# sw_sharps chokes if there is only one graphics card
if method == 'sw_sharp': no_threads = 1
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species(cursor)
print('=======================================')
print(sys.argv[0])
if special:
print("using", special, "set")
if special == 'complement':
gene_list = get_complement_ids(cursor, ensembl_db_name, cfg)
else:
gene_list = get_theme_ids(cursor, ensembl_db_name, cfg, special)
else:
print("using all protein coding genes")
switch_to_db(cursor, ensembl_db_name['homo_sapiens'])
gene_list = get_gene_ids(cursor, biotype='protein_coding', is_known=1)
cursor.close()
db.close()
parallelize(no_threads, find_missing_exons, gene_list,
[local_db, ensembl_db_name, method])
return True
def main():
special = 'test'
no_threads = 10
method = 'usearch'
if len(sys.argv) > 1 and len(sys.argv)<4:
print "usage: %s <set name> <number of threads> <method>" % sys.argv[0]
exit(1)
elif len(sys.argv)==4:
special = sys.argv[1]
special = special.lower()
if special == 'none': special = None
no_threads = int(sys.argv[2])
method = sys.argv[3]
if not (method =='usearch' or method=='sw_sharp'):
print "unrecognized method: ", method
exit(1)
# sw_sharps chokes if there is only one graphics card
if method=='sw_sharp': no_threads = 1
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
print '======================================='
print sys.argv[0]
if special:
print "using", special, "set"
if special == 'complement':
gene_list = get_complement_ids(cursor, ensembl_db_name, cfg)
else:
gene_list = get_theme_ids (cursor, ensembl_db_name, cfg, special )
else:
print "using all protein coding genes"
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
gene_list = get_gene_ids (cursor, biotype='protein_coding', is_known=1)
cursor.close()
db.close()
parallelize (no_threads, find_missing_exons, gene_list, [local_db, ensembl_db_name, method])
return True
def main():
no_threads = 10
db = connect_to_mysql()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
cursor.close()
db .close()
parallelize (no_threads, multiple_exon_alnmt, all_species, [local_db, ensembl_db_name])
return True
def main():
no_threads = 10
db = connect_to_mysql()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
species = 'homo_sapiens'
switch_to_db (cursor, ensembl_db_name[species])
gene_list = get_gene_ids (cursor, biotype='protein_coding', is_known=1)
cursor.close()
db.close()
parallelize (no_threads, collect_orthologues, gene_list, [local_db, ensembl_db_name])
return True
def main():
no_threads = 1
local_db = False
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species(cursor)
outdir = "{0}/para_dump".format(cfg.dir_path['afs_dumps'])
print outdir
if not os.path.exists(outdir):
print outdir, "not found"
exit(1) # exit after dir existence check
cursor.close()
db.close()
parallelize(no_threads, dump_paralogues, all_species,
[local_db, ensembl_db_name, outdir])
return True
def main():
no_threads = 1
local_db = False
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
outdir = "{0}/para_dump".format(cfg.dir_path['afs_dumps'])
print outdir
if not os.path.exists(outdir):
print outdir, "not found"
exit(1) # exit after dir existence check
cursor.close()
db .close()
parallelize (no_threads, dump_paralogues, all_species, [local_db, ensembl_db_name, outdir])
return True