From d6559a65865ebbb14e041893c2dae742fa146143 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 22 Aug 2020 16:41:02 +0200
Subject: genbank/sra scripts updated to read the dictionaries in a more
 general way

---
 scripts/create_sra_metadata/create_sra_metadata.py           | 12 ++++++++++--
 .../download_genbank_data/from_genbank_to_fasta_and_yaml.py  |  8 +++++---
 2 files changed, 15 insertions(+), 5 deletions(-)

(limited to 'scripts')

diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 352a30e..d02fde8 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -23,14 +23,19 @@ term_to_uri_dict = {}
 for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]:
     print('Read {}'.format(path_dict_xxx_csv))
 
-    with open(path_dict_xxx_csv, 'r') as f:
+    with open(path_dict_xxx_csv) as f:
         for line in f:
             if len(line.split(',')) > 2:
                 term, uri = line.strip('\n').split('",')
-                term = term.strip('"')
             else:
                 term, uri = line.strip('\n').split(',')
 
+            term = term.strip('"')
+
+            if term in term_to_uri_dict:
+                print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
+                continue
+
             term_to_uri_dict[term] = uri
 
 def is_integer(string_to_check):
@@ -178,6 +183,9 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
                         else:
                             info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(VALUE_text)
             elif TAG_text == 'geo_loc_name':
+                if ': ' in VALUE_text:
+                    VALUE_text = VALUE_text.replace(': ', ':')
+
                 if VALUE_text in term_to_uri_dict:
                     info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[VALUE_text]
                 elif VALUE_text.lower() not in ['na', 'not applicable']:
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index dbebfbb..3c59f8c 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -121,10 +121,11 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
         for line in f:
             if len(line.split(',')) > 2:
                 term, uri = line.strip('\n').split('",')
-                term = term.strip('"')
             else:
                 term, uri = line.strip('\n').split(',')
 
+            term = term.strip('"')
+
             if term in term_to_uri_dict:
                 print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
                 continue
@@ -243,6 +244,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                     GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
 
                     if GBQualifier_name_text == 'host':
+                        GBQualifier_value_text = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female
                         if GBQualifier_value_text in term_to_uri_dict:
                             # Cases like 'Felis catus; Domestic Shorthair'
                             info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text]
@@ -353,8 +355,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
 
                         info_for_yaml_dict['sample']['collection_date'] = date_to_write
                     elif GBQualifier_name_text in ['lat_lon', 'country']:
-                        if GBQualifier_value_text == 'Hong Kong':
-                            GBQualifier_value_text = 'China: Hong Kong'
+                        if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text:
+                            GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':')
 
                         if GBQualifier_value_text in term_to_uri_dict:
                             info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[GBQualifier_value_text]
-- 
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