Merge pull request #102 from AndreaGuarracino/patch-4

a lot of new ontology terms, genbank/sra scripts updated to be more general

1 files changed, 9 insertions, 5 deletions

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..f314a1d 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]
@@ -314,10 +316,12 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                         if GBQualifier_value_text in term_to_uri_dict:
                             info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[GBQualifier_value_text]]
                         else:
-                            if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab']:
+                            if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']:
                                 info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']]
-                            elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab']:
+                            elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']:
                                 info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']]
+                            elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']:
+                                info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']]
                             elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']:
                                 info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']]
                             elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
@@ -353,8 +357,8 @@ 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]