diff options
Diffstat (limited to 'Code/download_and_map.py')
| -rw-r--r-- | Code/download_and_map.py | 29 |
1 files changed, 2 insertions, 27 deletions
diff --git a/Code/download_and_map.py b/Code/download_and_map.py index dd063e1..f7e7d94 100644 --- a/Code/download_and_map.py +++ b/Code/download_and_map.py @@ -19,12 +19,11 @@ import fnmatch import time import re import shutil -import redis import json from datetime import datetime ########################################################################################## -from configure import DAILY_MAP_NUMBER, MIN_FASTQ_FILE_SIZE, RNA_SEQ_INFO_FILE, DOWNLOADED_SRA_ID_LOG_FILE, IGNORED_SRA_ID_LOG_FILE, UPDATE_NETWORK_LOG_FILE, MAPPED_RDATA_DIR, RAW_RDATA_DIR, SALMON_MAP_RESULT_DIR, REDIS_CHANNEL +from configure import DAILY_MAP_NUMBER, MIN_FASTQ_FILE_SIZE, RNA_SEQ_INFO_FILE, DOWNLOADED_SRA_ID_LOG_FILE, IGNORED_SRA_ID_LOG_FILE, UPDATE_NETWORK_LOG_FILE, MAPPED_RDATA_DIR, RAW_RDATA_DIR, SALMON_MAP_RESULT_DIR ########################################################################################## def glob_files(directory, pattern): @@ -387,22 +386,6 @@ def reverse_lines(fname, fname2): f2.write(content) -def publish(mapped_data_directory): - redis_host = os.getenv('REDIS_HOST', '127.0.0.1') - redis_password = os.getenv('REDIS_PASSWORD', '123456') - r = redis.Redis(host=redis_host, port=6379, password=redis_password, db=0) - r.publish(REDIS_CHANNEL, json.dumps({'filename':'REDIS_START.txt', 'data':str(datetime.now())})) - time.sleep(3) - for fname in glob.glob('%s/*_quant.txt' % (mapped_data_directory.rstrip('/'))): - try: - file_basename = os.path.basename(fname) - with open(fname, 'r') as f: - data = f.read() - r.publish(REDIS_CHANNEL, json.dumps({'filename':file_basename, 'data':data})) - except Exception as e: - r.publish(REDIS_CHANNEL, json.dumps({'filename':'REDIS_ERROR.txt', 'data':str(e)})) - time.sleep(3) - ## main # For filtering RNA-seq data @@ -451,16 +434,8 @@ curr_time = datetime.now().strftime('%Y-%m-%d_%H%M') # append date info to newly if not os.path.isdir(MAPPED_RDATA_DIR): os.makedirs(MAPPED_RDATA_DIR) -# after mapping is finished, move all resulting files to MAPPED_RDATA_DIR +# after mapping is finished, copy all resulting files to MAPPED_RDATA_DIR if glob.glob('%s/*_quant.txt' % (SALMON_MAP_RESULT_DIR.rstrip('/'))) != []: - - try: - write_network_log_file('[download_and_map.py] Ready to publish quant files.', UPDATE_NETWORK_LOG_FILE) - publish(SALMON_MAP_RESULT_DIR) - time.sleep(5) - except Exception as e: - write_network_log_file('[download_and_map.py] Publish error %s.' % (str(e)), UPDATE_NETWORK_LOG_FILE) - cmd = 'cp %s/*_quant.txt %s' % (SALMON_MAP_RESULT_DIR.rstrip('/'), MAPPED_RDATA_DIR) os.system(cmd) print('[download_and_map.py] Done. Check directory %s.' % (os.path.abspath(MAPPED_RDATA_DIR))) |