Save RNA_SEQ_INFO_DATABASE; do not need commland-line redirect now.

1 files changed, 10 insertions, 5 deletions

diff --git a/Code/parse_ena_xml.py b/Code/parse_ena_xml.py
index 4af3a77..8cb7946 100644
--- a/Code/parse_ena_xml.py
+++ b/Code/parse_ena_xml.py
@@ -1,4 +1,4 @@
-# Usage: python parse_ena_xml.py > rnaseq_info_database.txt
+# Usage: python parse_ena_xml.py
 #
 # Search in this script for 'd_run', 'd_sample', 'd_experiment' and
 # 'd_study', and set their input files.  The input files are generated
@@ -32,7 +32,7 @@ import sys
 import string
 import shutil
 from backup_files import backup_file
-from configure import ENA_RECORDS_READ_RUN, ENA_RECORDS_READ_EXPERIMENT, ENA_RECORDS_SAMPLE, ENA_RECORDS_STUDY, RNA_SEQ_INFO_DATABASE_JSON
+from configure import ENA_RECORDS_READ_RUN, ENA_RECORDS_READ_EXPERIMENT, ENA_RECORDS_SAMPLE, ENA_RECORDS_STUDY, RNA_SEQ_INFO_DATABASE, RNA_SEQ_INFO_DATABASE_JSON
 MAX_DESCRIPTION_LENGTH = 6000 # max number to characters to keep in json file
 
 
@@ -269,8 +269,11 @@ if __name__ == '__main__':
 
     cmd = 'export PYTHONIOENCODING=UTF-8'  # since xml files contains non-ascii characters, use this command to avoid encoding error during redirection
     os.system(cmd)
-    
-    print('%s' % ('\t'.join(['run_id', 'sample_id', 'experiment_id', 'study_id', 'study_id_PRJ', 'title', 'alias', 'description', 'library_strategy', 'library_source']))) # description comes from three sources, STUDY, SAMPLE and EXPERIMENT
+
+    backup_file(RNA_SEQ_INFO_DATABASE)
+    f = open(RNA_SEQ_INFO_DATABASE, 'w', encoding='utf-8')
+
+    f.write('%s\n' % ('\t'.join(['run_id', 'sample_id', 'experiment_id', 'study_id', 'study_id_PRJ', 'title', 'alias', 'description', 'library_strategy', 'library_source']))) # description comes from three sources, STUDY, SAMPLE and EXPERIMENT
 
     d_run_keys = d_run.keys()
     d_run_keys = list(set(d_run_keys))
@@ -299,7 +302,9 @@ if __name__ == '__main__':
         lst.append(description)
         lst.append(library_strategy)
         lst.append(library_source)
-        print('%s' % ('\t'.join(lst)))
+        f.write('%s\n' % ('\t'.join(lst)))
+
+    f.close()
 
     # Make a json file as well. this file is used to display rna-seq information in scatterplots.
     json_dict = {}