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| author | AndreaGuarracino | 2020-07-10 15:39:02 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-07-10 15:39:02 +0200 |
| commit | 2eab71a70b8630649303a9319e1baf9fa06f8ab4 (patch) | |
| tree | 02d6fed548b09381ef2de611d83a89647bd0594a /scripts/create_sra_metadata | |
| parent | 8cb542fdf60273aec7ec107f8bc4896375381263 (diff) | |
| download | bh20-seq-resource-2eab71a70b8630649303a9319e1baf9fa06f8ab4.tar.gz bh20-seq-resource-2eab71a70b8630649303a9319e1baf9fa06f8ab4.tar.lz bh20-seq-resource-2eab71a70b8630649303a9319e1baf9fa06f8ab4.zip | |
metadata with missing host_species are not created
Diffstat (limited to 'scripts/create_sra_metadata')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 5 |
1 files changed, 5 insertions, 0 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 10ac85b..a31bd36 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -242,6 +242,11 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): not_created_accession_list.append([accession, 'technology not found']) continue + if 'host_species' not in info_for_yaml_dict['host']: + #print(accession, ' - technology not found') + not_created_accession_list.append([accession, 'missing host species']) + continue + with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw: json.dump(info_for_yaml_dict, fw, indent=2) |