aboutsummaryrefslogtreecommitdiff
path: root/scripts
diff options
context:
space:
mode:
authorAndreaGuarracino2020-11-15 11:36:25 +0100
committerAndreaGuarracino2020-11-15 11:36:25 +0100
commit72e77fda220e939676d10fd8505fd15517e99702 (patch)
treef1e9b36e7e68a31df5a598d57063d26c1611c295 /scripts
parentba8c23625dea3d869eab821007e8f5db2eaf9dfe (diff)
downloadbh20-seq-resource-72e77fda220e939676d10fd8505fd15517e99702.tar.gz
bh20-seq-resource-72e77fda220e939676d10fd8505fd15517e99702.tar.lz
bh20-seq-resource-72e77fda220e939676d10fd8505fd15517e99702.zip
added a check on host_age
Diffstat (limited to 'scripts')
-rw-r--r--scripts/create_sra_metadata/create_sra_metadata.py2
-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py2
2 files changed, 2 insertions, 2 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index df77daf..83a1a60 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -179,7 +179,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
elif TAG_text in ['host_age', 'host age']:
if is_integer(VALUE_text):
host_age = is_integer(VALUE_text)
- if host_age > 0 and host_age < 110:
+ 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':
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 f9cc3fa..17b741a 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 > 0 and host_age < 110:
+ 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: