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authorAndreaGuarracino2020-08-22 16:41:02 +0200
committerAndreaGuarracino2020-08-22 16:41:02 +0200
commitd6559a65865ebbb14e041893c2dae742fa146143 (patch)
tree7e6f7e90038c457d5d6c0c0a180eba86393e1dbd /scripts
parent19c8d1390707c59f6acc26d23c78d462e4085a7b (diff)
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genbank/sra scripts updated to read the dictionaries in a more general way
Diffstat (limited to 'scripts')
-rw-r--r--scripts/create_sra_metadata/create_sra_metadata.py12
-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py8
2 files changed, 15 insertions, 5 deletions
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]