def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Some needed variables
processed_data_dir = opts.processed_data_dir
debug = opts.debug
# Get results for all processed_data_ folders in this study's directory
processed_results = summarize_all_stats(processed_data_dir)
submit_mapping_to_database(processed_results, debug)
from data_access_connections import data_access_factory
from enums import ServerConfig
from summarize_seqs_otu_hits import summarize_all_stats
import traceback
data_access = data_access_factory(ServerConfig.data_access_type)
query = 'select distinct sa.study_id from sample sa inner join sff.analysis a on sa.study_id = a.study_id order by study_id desc'
results = data_access.dynamicMetadataSelect(query)
debug = True
for result in results:
study_id = result[0]
try:
print 'Updating study {0}'.format(study_id)
# Get results for all processed_data_ folders in this study's directory
processed_results = summarize_all_stats(study_id)
submit_mapping_to_database(processed_results)
except OSError, os:
# Study dir doesn't exist on server - fine to just ignore
pass
except Exception, e:
print 'Could not process study_id: {0}. The error was: "{1}"'.format(study_id, str(e))
from summarize_seqs_otu_hits import summarize_all_stats, submit_mapping_to_database
from optparse import OptionParser
from os import walk, remove
from os.path import join, exists
parser = OptionParser()
#parser.add_option("-i", "--input_dir", dest="input directory", help="Processed data directory to summarize and load into db")
parser.add_option("-s", dest="study_id", help="The study_id to summarize seqs and otu stats for")
(options, args) = parser.parse_args()
study_id = options.study_id
base_dir = "/home/wwwuser/s/study_{0}/"
for dirname, dirnames, filenames in walk(base_dir.format(study_id)):
for d in dirnames:
if d.startswith('processed_data_'):
processed_dir = join(base_dir.format(study_id), d)
per_library_stats_file = join(processed_dir, 'gg_97_otus', 'per_library_stats.txt')
if exists(per_library_stats_file):
print 'Removing old per_library_stats.txt file: "{0}"'.format(per_library_stats_file)
remove(per_library_stats_file)
print 'Summarizing results for: "{0}"'.format(processed_dir)
processed_results = summarize_all_stats(processed_dir)
print 'Writing seqs and otu summary to database...'
submit_mapping_to_database(processed_results)
print 'Seq and OTU summary results successfully added to database.'
