def sample_ids2intron_ids_from_db(sample_ids):
select = 'SELECT snaptron_ids FROM by_sample_id WHERE sample_id in'
found_snaptron_ids = set()
results = snaputil.retrieve_from_db_by_ids(sc,select,sample_ids)
#ids = [x[0] for x in results]
for snaptron_ids in results:
found_snaptron_ids.update(set(snaptron_ids[0].split(',')))
#s1=','.join(ids)
#found_snaptron_ids.update(s1.split(','))
if '' in found_snaptron_ids:
found_snaptron_ids.remove('')
return found_snaptron_ids
def sample_ids2intron_ids_from_db(sample_ids):
select = 'SELECT snaptron_ids FROM by_sample_id WHERE sample_id in'
found_snaptron_ids = set()
results = snaputil.retrieve_from_db_by_ids(sc,select,sample_ids)
#ids = [x[0] for x in results]
for snaptron_ids in results:
found_snaptron_ids.update(set(snaptron_ids[0].split(',')))
#s1=','.join(ids)
#found_snaptron_ids.update(s1.split(','))
if '' in found_snaptron_ids:
found_snaptron_ids.remove('')
return found_snaptron_ids
def search_introns_by_ids(ids,rquery,filtering=False,region_args=default_region_args):
ra = region_args
select = 'SELECT * from intron WHERE snaptron_id in'
found_snaptron_ids = set()
if len(ids) == 0:
return (set(),set())
results = snaputil.retrieve_from_db_by_ids(snc,select,ids)
#now get methods for 1) header output and 2) intron output (depending on request)
(header_method,streamer_method) = return_formats[ra.return_format]
header_method(sys.stdout,region_args=ra,interval=ra.coordinate_string)
#exit early as we only want the ucsc_url
if ra.return_format == UCSC_URL:
return (set(),set())
for intron in results:
found_snaptron_ids.update(set([str(intron[0])]))
if ra.stream_back:
streamer_method(sys.stdout,None,intron,ra)
return (found_snaptron_ids,set())
def search_introns_by_ids(ids,rquery,filtering=False,region_args=default_region_args):
#TODO also process rquery as part of the SQL
ra = region_args
select = 'SELECT * from intron WHERE snaptron_id in'
found_snaptron_ids = set()
if len(ids) == 0:
return (set(),set())
results = snaputil.retrieve_from_db_by_ids(snc,select,ids)
#now get methods for 1) header output and 2) intron output (depending on request)
(header_method,streamer_method) = snaputil.return_formats[ra.return_format]
header_method(sys.stdout,region_args=ra,interval=ra.coordinate_string)
#exit early as we only want the ucsc_url
if ra.return_format == UCSC_URL:
return (set(),set())
for intron in results:
found_snaptron_ids.update(set([str(intron[0])]))
if ra.stream_back:
streamer_method(sys.stdout,None,intron,ra)
return (found_snaptron_ids,set())
def get_samples_for_snaptron_ids(ids):
select = 'SELECT snaptron_id,samples,read_coverage_by_sample FROM intron where snaptron_id in'
results = snaputil.retrieve_from_db_by_ids(sc,select,ids)
return results