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 = 1
special = ''
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
species = ''
if len(sys.argv) > 1 and len(sys.argv)<3 or len(sys.argv) >= 2 and sys.argv[1]=="-h":
print "usage: %s <set name/species> <number of processes>" % sys.argv[0]
exit(1) # after usage statement
elif len(sys.argv)==3:
special = sys.argv[1].lower()
if special == 'none':
special = None
elif special in all_species:
species = special
no_threads = int(sys.argv[2])
print '======================================='
print sys.argv[0]
if species:
print species, "only"
switch_to_db (cursor, ensembl_db_name[species])
if (species=='homo_sapiens'):
gene_ids = get_gene_ids (cursor, biotype='protein_coding', is_known=1, ref_only=True)
else:
gene_ids = get_gene_ids (cursor, biotype='protein_coding')
parallelize_args = [no_threads, one_species_all_genes_loop, gene_ids, [local_db, ensembl_db_name, species]]
elif special:
print "using", special, "set"
gene_list = get_theme_ids (cursor, ensembl_db_name, cfg, special )
parallelize_args = [no_threads, ortologues_for_given_genes_loop, gene_list, [local_db, ensembl_db_name]]
else:
parallelize_args = [no_threads, all_species_all_genes_loop, all_species, [local_db, ensembl_db_name]]
cursor.close()
db .close()
parallelize (*parallelize_args)
def main():
no_threads = 10
special = None
if len(sys.argv) > 1 and len(sys.argv)<3:
print "usage: %s <set name> <number of threads> " % sys.argv[0]
exit(1)
elif len(sys.argv)==3:
special = sys.argv[1]
special = special.lower()
if special == 'none': special = None
no_threads = int(sys.argv[2])
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"
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, maps_for_gene_list, gene_list, [local_db, ensembl_db_name])
return True
def main():
"""
Main entry point, but in reality does nothing except taking care of the parallelization.
The parallelization here is per-species.
"""
no_threads = 1
special = ''
if len(sys.argv) > 1 and len(sys.argv)<3 or len(sys.argv) >= 2 and sys.argv[1]=="-h":
print "usage: %s <set name> <number of threads>" % sys.argv[0]
exit(1) # after usage statment
elif len(sys.argv)==3:
special = sys.argv[1].lower()
if special == 'none': special = None
no_threads = int(sys.argv[2])
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"
gene_list = get_theme_ids (cursor, ensembl_db_name, cfg, special )
cursor.close()
db .close()
# two version of the main loop:
# 1) over all species, and all genes in each speceis
if not special:
parallelize (no_threads, store_exon_seqs, all_species, [local_db, ensembl_db_name])
else:
parallelize (no_threads, store_exon_seqs_special, gene_list, [local_db, ensembl_db_name])
def main():
special = None
no_threads = 1
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
[all_species, ensembl_db_name] = get_species (cursor)
if special:
print "using", special, "set"
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)
# loop over all genes
sw_count = 0
tot_count = 0
for human_gene_id in gene_list:
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
human_stable = gene2stable (cursor, human_gene_id)
human_description = get_description(cursor, human_gene_id)
tot_count += 1
#print human_gene_id, human_stable, human_description
human_exons = [e for e in gene2exon_list(cursor, human_gene_id, verbose=True)
if e.covering_exon < 0 and e.is_canonical and e.is_known]
if not human_exons:
#print "\t\t", human_stable, "no exons found"
continue
human_exons.sort(key=lambda exon: exon.start_in_gene)
# loop over all exons in this gene
maps_for_exon = {}
for he in human_exons:
he.stable_id = exon2stable (cursor, he.exon_id, ensembl_db_name['homo_sapiens'])
he.pepseq = get_exon_pepseq (cursor, he, ensembl_db_name['homo_sapiens'])
# maps cleanup: get rid of maps that have "none" as similarity
maps_for_exon[he] = get_maps(cursor, ensembl_db_name, he.exon_id, he.is_known) # exon data
if not maps_for_exon[he]: continue
#maps_for_exon[he] = filter (lambda m: m.source == 'sw_sharp' or m.source == 'usearch',
# maps_for_exon[he])
maps_for_exon[he] = filter (lambda m: m.source == 'usearch',
maps_for_exon[he])
if not maps_for_exon[he]:
#print "\t\t", human_stable, "no maps found"
continue
sw_count += len(maps_for_exon[he])
#break
print "tot count: ", tot_count
print "sw count: ", sw_count
#print "tot count: ", tot_count
#print "sw count: ", sw_count
cursor.close()
db.close()
def main():
no_threads = 1
special = None
if len(sys.argv) > 1 and len(sys.argv) < 3:
print "usage: %s <set name> <number of threads> " % sys.argv[0]
exit(1)
elif len(sys.argv) == 3:
special = sys.argv[1]
special = special.lower()
if special == 'none': special = None
no_threads = int(sys.argv[2])
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
# find db ids adn common names for each species db
[all_species, ensembl_db_name] = get_species(cursor)
species = 'homo_sapiens'
switch_to_db(cursor, ensembl_db_name[species])
if special:
print "using", special, "set"
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)
incomplete = 0
genes_checked = 0
#for gene_id in gene_list:
#for gene_id in [743609]:
for sampling_count in range(1000):
gene_id = choice(gene_list)
genes_checked += 1
with_map = 0
tot = 0
switch_to_db(cursor, ensembl_db_name['homo_sapiens'])
print gene2stable(cursor, gene_id), get_description(cursor, gene_id)
# find all exons we are tracking in the database
human_exons = gene2exon_list(cursor, gene_id)
human_exons.sort(key=lambda exon: exon.start_in_gene)
has_a_map = False
for human_exon in human_exons:
if (not human_exon.is_canonical or not human_exon.is_coding):
continue
if verbose:
print
print "\t human", human_exon.exon_id, human_exon.is_known
print "\t ", get_exon_pepseq(cursor, human_exon,
ensembl_db_name['homo_sapiens'])
print "\t checking maps ..."
maps = get_maps(cursor, ensembl_db_name, human_exon.exon_id,
human_exon.is_known)
tot += 1
if maps:
has_a_map = True
with_map += 1
#print "ok"
else:
print "no maps for exon", human_exon.exon_id
continue
if verbose:
for map in maps:
species = map.species_2
exon = map2exon(cursor, ensembl_db_name, map)
unaligned_sequence = get_exon_pepseq(
cursor, exon, ensembl_db_name[species])
if (map.similarity):
print "\t", species, map.source, map.exon_id_2, map.exon_known_2
print "\tmaps to ", map.exon_id_1, map.exon_known_1
print "\tsim", map.similarity,
print "\tsource", map.source
print "\t", unaligned_sequence
if not map.bitmap:
print "\t bitmap not assigned"
else:
bs = Bits(bytes=map.bitmap)
reconst_pepseq = ''
if (not bs.count(1) == len(unaligned_sequence)):
print "\talnd seq mismatch"
else:
usi = iter(unaligned_sequence)
for c in bs.bin:
if c == '0': reconst_pepseq += '-'
else: reconst_pepseq += next(usi)
print "\tbinary : ", bs.bin
print "\talnd seq: ", reconst_pepseq
print
if not tot == with_map:
print "#### gene id: %d total exons: %d with map: %d ( = %d%%) " % \
(gene_id, tot, with_map, int(float(with_map)/tot*100) )
incomplete += 1
print "genes checked: %d, incomplete: %d" % (genes_checked, incomplete)
cursor.close()
db.close()
print tot, with_map
def main():
no_threads = 1
special = None
if len(sys.argv) > 1 and len(sys.argv)<3:
print "usage: %s <set name> <number of threads> " % sys.argv[0]
exit(1)
elif len(sys.argv)==3:
special = sys.argv[1]
special = special.lower()
if special == 'none': special = None
no_threads = int(sys.argv[2])
db = connect_to_mysql()
cfg = ConfigurationReader()
cursor = db.cursor()
# find db ids adn common names for each species db
[all_species, ensembl_db_name] = get_species (cursor)
species = 'homo_sapiens'
switch_to_db (cursor, ensembl_db_name[species])
if special:
print "using", special, "set"
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)
incomplete = 0
genes_checked = 0
#for gene_id in gene_list:
#for gene_id in [743609]:
for sampling_count in range(1000):
gene_id = choice(gene_list)
genes_checked += 1
with_map = 0
tot = 0
switch_to_db (cursor, ensembl_db_name['homo_sapiens'])
print gene2stable(cursor, gene_id), get_description (cursor, gene_id)
# find all exons we are tracking in the database
human_exons = gene2exon_list(cursor, gene_id)
human_exons.sort(key=lambda exon: exon.start_in_gene)
has_a_map = False
for human_exon in human_exons:
if (not human_exon.is_canonical or not human_exon.is_coding): continue
if verbose:
print
print "\t human", human_exon.exon_id, human_exon.is_known
print "\t ", get_exon_pepseq(cursor, human_exon, ensembl_db_name['homo_sapiens'])
print "\t checking maps ..."
maps = get_maps(cursor, ensembl_db_name, human_exon.exon_id, human_exon.is_known)
tot += 1
if maps:
has_a_map = True
with_map += 1
#print "ok"
else:
print"no maps for exon", human_exon.exon_id
continue
if verbose:
for map in maps:
species = map.species_2
exon = map2exon(cursor, ensembl_db_name, map)
unaligned_sequence = get_exon_pepseq(cursor, exon, ensembl_db_name[species])
if ( map.similarity):
print "\t", species, map.source, map.exon_id_2, map.exon_known_2
print "\tmaps to ", map.exon_id_1, map.exon_known_1
print "\tsim", map.similarity,
print "\tsource", map.source
print "\t", unaligned_sequence
if not map.bitmap:
print "\t bitmap not assigned"
else:
bs = Bits(bytes=map.bitmap)
reconst_pepseq = ''
if (not bs.count(1) == len(unaligned_sequence)):
print "\talnd seq mismatch"
else:
usi = iter(unaligned_sequence)
for c in bs.bin:
if c == '0': reconst_pepseq += '-'
else: reconst_pepseq += next(usi)
print "\tbinary : ", bs.bin
print "\talnd seq: ", reconst_pepseq
print
if not tot== with_map:
print "#### gene id: %d total exons: %d with map: %d ( = %d%%) " % \
(gene_id, tot, with_map, int(float(with_map)/tot*100) )
incomplete += 1
print "genes checked: %d, incomplete: %d" % (genes_checked, incomplete)
cursor.close()
db.close()
print tot, with_map
