Regular maintenanceHEADmaster

1 files changed, 4 insertions, 2 deletions

diff --git a/Code/download_and_map.py b/Code/download_and_map.py
index bb46c81..42e9fb0 100644
--- a/Code/download_and_map.py
+++ b/Code/download_and_map.py
@@ -81,6 +81,7 @@ def make_download_list(mapped_dir, rna_data_info_dict, experiment_library_info_d
     all_run_ids - a list of NextGen-Seq IDs to select from, not necessarily RNA-seq 
     mapped_dir - contain all mapped samples
     rna_data_info_dict - a dictionary containing all RNA-seq samples from ENA.
+    experiment_library_info_dict - a dictionary containing library strategy/source info for experiment ids
     '''
 
     result = []
@@ -91,9 +92,9 @@ def make_download_list(mapped_dir, rna_data_info_dict, experiment_library_info_d
         include_me_because_i_am_rnaseq = True if rna_data_info_dict[run_id]['library_strategy'].lower() == 'rna-seq' and  rna_data_info_dict[run_id]['library_source'].lower() == 'transcriptomic' else False
         associated_experiment_id = rna_data_info_dict[run_id]['experiment_id']
         if associated_experiment_id in experiment_library_info_dict:
-            is_rnaseq = 'rna-seq' in experiment_library_info_dict[associated_experiment_id]['library_strategy'].lower() and 'transcriptomic' in experiment_library_info_dict[associated_experiment_id]['library_source']
+            is_rnaseq = 'rna-seq' in experiment_library_info_dict[associated_experiment_id]['library_strategy'].lower() and 'transcriptomic' in experiment_library_info_dict[associated_experiment_id]['library_source'].lower()
             include_me_because_i_am_rnaseq = include_me_because_i_am_rnaseq or is_rnaseq
-        if not (run_id + '_quant.txt') in mapped_files and (not run_id in result) and (not run_id in small_ids) and (not run_id in mapped_run_ids) and include_me_because_i_am_rnaseq: # not mapped yet and is RNA-seq
+        if include_me_because_i_am_rnaseq and not (run_id + '_quant.txt') in mapped_files and (not run_id in result) and (not run_id in small_ids) and (not run_id in mapped_run_ids): # is RNA-seq and not mapped yet
             result.append(run_id)
     return result
 
@@ -437,6 +438,7 @@ else:
     download_list = make_download_list(MAPPED_RDATA_DIR, rna_data_info_dict, experiment_library_info_dict)
     print('[download_and_map.py] There are %d run IDs from which you could select %d of them.' % (len(download_list), DAILY_MAP_NUMBER))
 
+
 # Make a record in log.txt
 curr_time = datetime.now().strftime('%Y-%m-%d_%H%M') # append date info to newly created directories
 write_download_log_file(DOWNLOADED_SRA_ID_LOG_FILE, 'START at %s (remaining %d)\n' % (curr_time, len(download_list)))