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| author | Hui Lan <lanhui@zjnu.edu.cn> | 2022-10-09 14:11:01 +0800 |
|---|---|---|
| committer | Hui Lan <lanhui@zjnu.edu.cn> | 2022-10-09 14:11:01 +0800 |
| commit | 8057467f9547afc07339a36cd2c05c170faffb3a (patch) | |
| tree | 2dff55a9d2b17f017acfac70fb7e88075ad2350a | |
| parent | ff5064e879ecba67f21da63b49982fc4060f8ec3 (diff) | |
Shorten config variable name, remove 'PARAMETER_FOR_'
| -rw-r--r-- | Code/configure.py | 2 | ||||
| -rwxr-xr-x | Code/update_network.py | 4 |
2 files changed, 3 insertions, 3 deletions
diff --git a/Code/configure.py b/Code/configure.py index 825cedc..3442bd4 100644 --- a/Code/configure.py +++ b/Code/configure.py @@ -33,7 +33,7 @@ PARAMETER_FOR_NET_WIGGELAB_DIURNAL = '../Data/parameter/parameter_for_net_wig BINDING_FILE = '../Data/history/bind/binding.txt'
TPM_FILE = '../Data/history/expr/TPM.txt' # gene expression data
-PARAMETER_FOR_BUILDRMATRIX_RENEW_INTERVAL = 18 # check every 18 days for updating TPM.txt
+BUILDRMATRIX_RENEW_INTERVAL = 1 # check every 18 days for updating TPM.txt
MIN_RNA_SEQ_INCREASE = -10000 # minimum RNA-seq experiments needed when updating parameter_for_buildRmatrix.txt
UPDATE_NETWORK_LOG_FILE = '../Data/log/update.network.log.txt' # network update log. We should check this file from time to time.
NEW_OR_UPDATED_CHIP_FILE = '../Data/log/new.or.updated.chip.file.txt'
diff --git a/Code/update_network.py b/Code/update_network.py index 13e1c11..542cbdf 100755 --- a/Code/update_network.py +++ b/Code/update_network.py @@ -51,7 +51,7 @@ from configure import HISTORY_DIR, HISTORY_DIR2, FILE_TIMESTAMP, SAMPLE_SIZE_FIL PARAMETER_FOR_BUILDCMATRIX, PARAMETER_FOR_BUILDRMATRIX, \ PARAMETER_FOR_NET, PARAMETER_FOR_NET_TRAVADB_STRESS, PARAMETER_FOR_NET_TRAVADB_MAP, PARAMETER_FOR_NET_MILD_DROUGHT, PARAMETER_FOR_NET_WIGGELAB_DIURNAL, \ BINDING_FILE, TPM_FILE, \ - PARAMETER_FOR_BUILDRMATRIX_RENEW_INTERVAL, MIN_RNA_SEQ_INCREASE, UPDATE_NETWORK_LOG_FILE, NEW_OR_UPDATED_CHIP_FILE, \ + BUILDRMATRIX_RENEW_INTERVAL, MIN_RNA_SEQ_INCREASE, UPDATE_NETWORK_LOG_FILE, NEW_OR_UPDATED_CHIP_FILE, \ RNA_SEQ_INFO_DATABASE, RNA_SEQ_INFO_DATABASE_JSON, GENE_ID_FIRST_TWO_LETTERS, MEMORY_STRENGTH, \ MAPPED_RDATA_DIR, MAPPED_CDATA_DIR, \ EDGE_POOL_DIR, MERGED_EDGE_FILE, \ @@ -691,7 +691,7 @@ if 'binding.txt' in updated_file_list: ################## TPM.txt stuff ##################################### # update parameter_for_buildRmatrix.txt periodically and automatically. -if datetime.now().day % PARAMETER_FOR_BUILDRMATRIX_RENEW_INTERVAL == 0: # check if need to update parameter_for_buildRmatrix.txt bi-weekly +if datetime.now().day % BUILDRMATRIX_RENEW_INTERVAL == 0: # check if need to update parameter_for_buildRmatrix.txt bi-weekly curr_time = datetime.now().strftime('%Y%m%d%H%M') new_parameter_file = '../Data/temp/parameter_for_buildRmatrix.%s' % (curr_time) cmd = 'python3 make_parameter_rnaseq.py > %s' % (new_parameter_file) # new_parameter_file will not be updated unless download_and_map.py has finished. |