def main(argv):
parser = argparse.ArgumentParser(
description=
'add_primer_to_annotations.py version %s\nupdate the primer region on the dbbact annotations'
% __version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--log-level',
help='output level (1 verbose, 10 error)',
type=int,
default=3)
parser.add_argument(
'--all',
help=
'update all annotations (if not specified, update only annotations with na in primer)',
action='store_true')
args = parser.parse_args(argv)
SetDebugLevel(args.log_level)
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
add_primer_to_annotations(con, cur, update_all=args.all)
def main(argv):
parser = argparse.ArgumentParser(
description=
'Add annotation/experiment counts to all dbbact sequences. version ' +
__version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--proc-title',
help='name of the process (to view in ps aux)')
parser.add_argument('--debug-level',
help='debug level (1 for debug ... 9 for critical)',
default=2,
type=int)
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
# set the process name for ps aux
if args.proc_title:
setproctitle.setproctitle(args.proc_title)
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
add_seq_counts(con, cur)
def main(argv):
parser = argparse.ArgumentParser(
description='Add the number of sequences per annotation. version ' +
__version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--debug-level',
help='debug level (1 for debug ... 9 for critical)',
default=2,
type=int)
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
add_annotation_seq_count(con, cur)
def om_cmd(ctx, database, port, host, user, password, debug_level, log_file, dry_run):
con, cur = db_access.connect_db(database=database, user=user, password=password, port=port, host=host)
ctx.obj = {}
ctx.obj['con'] = con
ctx.obj['cur'] = cur
ctx.obj['debug_level'] = debug_level
ctx.obj['log_file'] = log_file
ctx.obj['commit'] = not dry_run
SetDebugLevel(debug_level)
def main(argv):
parser = argparse.ArgumentParser(description='delete_annotations version %s\ndelete sequences not in any annotation' % __version__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database', help='postgres database', default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password', help='postgres password', default='magNiv')
parser.add_argument('--annotationids', help='list of annotation ids to delete (space separated)', nargs='+', type=int)
parser.add_argument('--expids', help='list of experiment ids to delete (space separated)', nargs='+', type=int)
parser.add_argument('--delete', help='delete the sequences', action='store_true')
parser.add_argument('--noseq', help='delete only annotations where all sequences do not start with noseq (i.e. acgt to not delete v4)')
parser.add_argument('--log-level', help='output level (1 verbose, 10 error)', type=int, default=3)
args = parser.parse_args(argv)
SetDebugLevel(args.log_level)
con, cur = db_access.connect_db(database=args.database, user=args.user, password=args.password, port=args.port, host=args.host)
annotationids = []
# fill the annotations from each experiment
if args.expids:
for cexpid in args.expids:
cur.execute("SELECT id from AnnotationsTable WHERE idexp=%s", [cexpid])
for cres in cur:
annotationids.append(cres[0])
debug(3, 'found %d annotations for the experiments' % len(annotationids))
# and add the annotation ids supplied
if args.annotationids is not None:
annotationids.extend(args.annotationids)
for cannotationid in annotationids:
# test if all sequences of the annotation don't start with sequence notseq
if args.noseq is not None:
cur2 = con.cursor(cursor_factory=psycopg2.extras.DictCursor)
noseq = args.noseq
badseqs = 0
cur.execute("SELECT seqid FROM SequencesAnnotationTable WHERE annotationid=%s", [cannotationid])
for cres in cur:
cseqid = cres[0]
cur2.execute("SELECT sequence FROM SequencesTable WHERE id=%s", [cseqid])
res = cur2.fetchone()[0]
if res[:len(noseq)] == noseq:
badseqs += 1
if badseqs > 0:
debug(5, "Annotation %d contains %d sequences starting with the noseq sequenece %s. not deleting" % (cannotationid, badseqs, noseq))
continue
# get the user that created the annotation
cur.execute("SELECT iduser FROM AnnotationsTable WHERE id=%s LIMIT 1", [cannotationid])
res = cur.fetchone()
cuserid = res['iduser']
# and delete
delete_annotation(con, cur, annotationid=cannotationid, userid=cuserid, delete=args.delete)
debug(3, 'committing')
con.commit()
debug(3, 'done. please run delete_unused_seqs.py to remove unused sequences')
def main(argv):
parser = argparse.ArgumentParser(description='run_bg_jobs version %s.' % __version__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database', help='postgres database (overrides value from server-type)')
parser.add_argument('--user', help='postgres user (overrides value from server-type)')
parser.add_argument('--password', help='postgres password (overrides value from server-type)')
parser.add_argument('--server-type', help='dbbact rest api server type (main/develop/test)', default='main')
parser.add_argument('-o', '--output-dir', help='output directory for the log files')
parser.add_argument('--debug-level', help='debug level (1 for debug ... 9 for critical)', default=2, type=int)
parser.add_argument('--single-update', help='update once and quit', action='store_true')
parser.add_argument('-p', '--command-params', help='specific command parameters. command and parameter name separated by : (i.e. update_silva:wholeseq-file:SILVA.fa). can use flag more than once', action='append')
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
server_type = args.server_type
database = args.database
user = args.user
password = args.password
proc_title = 'dbbact run_bg_jobs.py'
if server_type == 'main':
proc_title += ' [main]'
if database is None:
database = 'dbbact'
if user is None:
user = '******'
if password is None:
password = '******'
elif server_type == 'develop':
proc_title += ' [develop]'
if database is None:
database = 'dbbact_develop'
if user is None:
user = '******'
if password is None:
password = '******'
elif server_type == 'test':
proc_title += ' [test]'
if database is None:
database = 'dbbact'
if user is None:
user = '******'
if password is None:
password = '******'
elif server_type is None:
pass
else:
raise ValueError('unknown server-type. should be one of ("main" / "develop" / "test"')
setproctitle.setproctitle(proc_title + ' [master]')
run_bg_jobs(port=args.port, host=args.host, database=database, user=user, password=password, single_update=args.single_update, command_params=args.command_params, debug_level=args.debug_level, output_dir=args.output_dir, proc_title=proc_title)
def main(argv):
parser = argparse.ArgumentParser(description='Prepare dbBact-calour term pickle files for autocomplete. version ' + __version__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database', help='postgres database', default='dbbact_develop')
parser.add_argument('--user', help='postgres user', default='dbbact_develop')
parser.add_argument('--password', help='postgres password', default='dbbact_develop')
parser.add_argument('--debug-level', help='debug level (1 for debug ... 9 for critical)', default=4, type=int)
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
con, cur = db_access.connect_db(database=args.database, user=args.user, password=args.password, port=args.port, host=args.host)
prepare_dbbact_calour_term_files(con, cur)
def main(argv):
parser = argparse.ArgumentParser(description='Update the OntologyTreeStructureTable to fix the old na root term (which was undefined as contained many optional NAs). version ' + __version__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database', help='postgres database', default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password', help='postgres password', default='magNiv')
parser.add_argument('--debug-level', help='debug level (1 for debug ... 9 for critical)', default=2, type=int)
parser.add_argument('--dry-run', help='do not commit', action='store_true')
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
con, cur = db_access.connect_db(database=args.database, user=args.user, password=args.password, port=args.port, host=args.host)
fix_na(con, cur, commit=not args.dry_run)
def main(argv):
parser = argparse.ArgumentParser(
description=
'Replace obsoloete ontology terms after running add_ontology. version '
+ __version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-i',
'--input',
help='ontology file name (.obo) to update with')
parser.add_argument(
'--ontology',
help=
'ontology database name (i.e. "envo"). if provided, only update terms not appearing in other ontologies',
default=None)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--proc-title',
help='name of the process (to view in ps aux)')
parser.add_argument('--debug-level',
help='debug level (1 for debug ... 9 for critical)',
default=2,
type=int)
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
# set the process name for ps aux
if args.proc_title:
setproctitle.setproctitle(args.proc_title)
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
update_obsolete_terms(con,
cur,
ontofilename=args.input,
ontology_name=args.ontology)
def main(argv):
parser = argparse.ArgumentParser(
description=
'Update the AnnotationParentsTable after changing ontologies. version '
+ __version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--proc-title',
help='name of the process (to view in ps aux)')
parser.add_argument('--debug-level',
help='debug level (1 for debug ... 9 for critical)',
default=2,
type=int)
parser.add_argument(
'--ontology',
help='ontology to update parents for (empty to update all')
parser.add_argument(
'--redo-all',
help='if set, recalculate for all ontologies/terms (slower)',
action='store_true')
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
# set the process name for ps aux
if args.proc_title:
setproctitle.setproctitle(args.proc_title)
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
if args.redo_all:
update_ontology_parents_overwrite(con, cur)
else:
update_ontology_parents(con, cur, ontology=args.ontology)
def main(argv):
parser = argparse.ArgumentParser(description='Delete dbbact terms not used in annotations or tree structure. version ' + __version__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database', help='postgres database', default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password', help='postgres password', default='magNiv')
parser.add_argument('--proc-title', help='name of the process (to view in ps aux)')
parser.add_argument('--delete', help='MUST provide this in order to actually delete', action='store_true')
parser.add_argument('--debug-level', help='debug level (1 for debug ... 9 for critical)', default=2, type=int)
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
# set the process name for ps aux
if args.proc_title:
setproctitle.setproctitle(args.proc_title)
con, cur = db_access.connect_db(database=args.database, user=args.user, password=args.password, port=args.port, host=args.host)
delete_unused_terms(con, cur, commit=args.delete)
def main(argv):
parser = argparse.ArgumentParser(
description=
'update_sequence_primer.py version %s\nupdate the sequence primer (merge if needed)'
% __version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--old-primer',
help='the primerid of sequences to update',
type=int,
default=2)
parser.add_argument('--new-primer',
help='the primerid to update to',
type=int,
default=1)
parser.add_argument('--log-level',
help='output level (1 verbose, 10 error)',
type=int,
default=3)
parser.add_argument('--delete',
help='delete the sequences',
action='store_true')
args = parser.parse_args(argv)
SetDebugLevel(args.log_level)
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
update_old_primer_seqs(con,
cur,
old_primer=args.old_primer,
new_primer=args.new_primer,
commit=args.delete)
def main(argv):
parser = argparse.ArgumentParser(
description='update_seq_hash version %s' % __version__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--port', help='postgres port', default=5432, type=int)
parser.add_argument('--host', help='postgres host', default=None)
parser.add_argument('--database',
help='postgres database',
default='dbbact')
parser.add_argument('--user', help='postgres user', default='dbbact')
parser.add_argument('--password',
help='postgres password',
default='magNiv')
parser.add_argument('--proc-title',
help='name of the process (to view in ps aux)')
parser.add_argument('--debug-level',
help='debug level (1 for debug ... 9 for critical)',
default=2,
type=int)
parser.add_argument('--rdp',
help='location of the rdp binary dir',
default='rdp_classifier_2.12/')
args = parser.parse_args(argv)
SetDebugLevel(args.debug_level)
# set the process name for ps aux
if args.proc_title:
setproctitle.setproctitle(args.proc_title)
# get the database connection
con, cur = db_access.connect_db(database=args.database,
user=args.user,
password=args.password,
port=args.port,
host=args.host)
update_seq_taxonomy(con, cur, rdp=args.rdp)
if password is None:
password = '******'
elif server_type == 'develop':
proc_title += ' [develop]'
if database is None:
database = 'dbbact_develop'
if user is None:
user = '******'
if password is None:
password = '******'
elif server_type == 'test':
proc_title += ' [test]'
if database is None:
database = 'dbbact'
if user is None:
user = '******'
if password is None:
password = '******'
elif server_type is None:
pass
else:
raise ValueError('unknown server-type. should be one of ("main" / "develop" / "test"')
setproctitle.setproctitle(proc_title + ' [master]')
run_bg_jobs(port=args.port, host=args.host, database=database, user=user, password=password, single_update=args.single_update, command_params=args.command_params, debug_level=args.debug_level, output_dir=args.output_dir, proc_title=proc_title)
if __name__ == "__main__":
SetDebugLevel(1)
main(sys.argv[1:])