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| author | AndreaGuarracino | 2020-11-14 23:30:53 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2020-11-14 23:30:53 +0100 |
| commit | ba8c23625dea3d869eab821007e8f5db2eaf9dfe (patch) | |
| tree | 30d256d8467bd41cbb91d35c1c1cf58066278182 /scripts | |
| parent | c5cc4e975e0d3a2ea1f296b63fdfddeddfd793ec (diff) | |
| download | bh20-seq-resource-ba8c23625dea3d869eab821007e8f5db2eaf9dfe.tar.gz bh20-seq-resource-ba8c23625dea3d869eab821007e8f5db2eaf9dfe.tar.lz bh20-seq-resource-ba8c23625dea3d869eab821007e8f5db2eaf9dfe.zip | |
added a check on host_age
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 6 | ||||
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 2 |
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: |