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authorAndreaGuarracino2020-11-14 23:30:53 +0100
committerAndreaGuarracino2020-11-14 23:30:53 +0100
commitba8c23625dea3d869eab821007e8f5db2eaf9dfe (patch)
tree30d256d8467bd41cbb91d35c1c1cf58066278182 /scripts
parentc5cc4e975e0d3a2ea1f296b63fdfddeddfd793ec (diff)
downloadbh20-seq-resource-ba8c23625dea3d869eab821007e8f5db2eaf9dfe.tar.gz
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added a check on host_age
Diffstat (limited to 'scripts')
-rw-r--r--scripts/create_sra_metadata/create_sra_metadata.py6
-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py2
2 files changed, 5 insertions, 3 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 89624fd..df77daf 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -178,8 +178,10 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
missing_value_list.append('\t'.join([accession, 'host_sex', VALUE_text]))
elif TAG_text in ['host_age', 'host age']:
if is_integer(VALUE_text):
- info_for_yaml_dict['host']['host_age'] = int(VALUE_text)
- info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
+ host_age = is_integer(VALUE_text)
+ if host_age > 0 and host_age < 110:
+ info_for_yaml_dict['host']['host_age'] = host_age
+ info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
elif TAG_text == 'collected_by':
if VALUE_text.lower() not in ['not available', 'missing']:
name = VALUE_text in ['Dr. Susie Bartlett', 'Ahmed Babiker', 'Aisi Fu', 'Brandi Williamson', 'George Taiaroa', 'Natacha Ogando', 'Tim Dalebout', 'ykut Ozdarendeli']
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 442a9a5..f9cc3fa 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
@@ -311,7 +311,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]):
host_age = int(GBQualifier_value_text_list[2].split(' ')[-1])
- if host_age > -1:
+ if host_age > 0 and host_age < 110:
info_for_yaml_dict['host']['host_age'] = host_age
info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
elif len(GBQualifier_value_text_list) > 2: