diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 8 | ||||
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 1 |
2 files changed, 4 insertions, 5 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 85d4e9e..f5dc0c8 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -290,10 +290,10 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')] collection_date_in_yaml = datetime(year, month, day) - - if accession not in not_created_accession_dict: - not_created_accession_dict[accession] = [] - not_created_accession_dict[accession].append('collection_date too early') + if collection_date_in_yaml < min_acceptable_collection_date: + if accession not in not_created_accession_dict: + not_created_accession_dict[accession] = [] + not_created_accession_dict[accession].append('collection_date too early') if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: # print(accession_version, ' - technology not found') 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 1352027..442a9a5 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 @@ -409,7 +409,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')] collection_date_in_yaml = datetime(year, month, day) - if collection_date_in_yaml < min_acceptable_collection_date: if accession_version not in not_created_accession_dict: not_created_accession_dict[accession_version] = [] |