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| author | Pjotr Prins | 2021-01-03 10:36:55 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-03 10:36:55 +0000 |
| commit | 0de0ae0ac62e85f1ba6587a252b5a1164cbd5210 (patch) | |
| tree | 79f9b1065ec8eb640eb50db9929a88aee2025daa /workflows/pull-data/genbank/ref.py | |
| parent | a10c61d1f5afca70f54b762beefb402372d7fd31 (diff) | |
| download | bh20-seq-resource-0de0ae0ac62e85f1ba6587a252b5a1164cbd5210.tar.gz bh20-seq-resource-0de0ae0ac62e85f1ba6587a252b5a1164cbd5210.tar.lz bh20-seq-resource-0de0ae0ac62e85f1ba6587a252b5a1164cbd5210.zip | |
genbank: deal with host, sex and age
Diffstat (limited to 'workflows/pull-data/genbank/ref.py')
| -rw-r--r-- | workflows/pull-data/genbank/ref.py | 48 |
1 files changed, 2 insertions, 46 deletions
diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py index d809d7f..a9b4f06 100644 --- a/workflows/pull-data/genbank/ref.py +++ b/workflows/pull-data/genbank/ref.py @@ -26,53 +26,9 @@ technology[field_in_yaml] = tech_info_to_parse - for GBFeature in GBSeq.iter('GBFeature'): - if GBFeature.find('GBFeature_key').text != 'source': - continue - - for GBQualifier in GBFeature.iter('GBQualifier'): - GBQualifier_value = GBQualifier.find('GBQualifier_value') - if GBQualifier_value is None: - continue - GBQualifier_value_text = GBQualifier_value.text - - GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text - - if GBQualifier_name_text == 'host': - GBQualifier_value_text = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female - if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']: - # Cases like 'Felis catus; Domestic Shorthair' - host['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text] - else: - GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']: - host['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text_list[0]] - elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version): - # Information checked manually from NCBI Virus - host['host_species'] = field_to_term_to_uri_dict['ncbi_host_species']['Canis lupus familiaris'] - else: - missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]])) - - # Possible cases: - # - Homo sapiens --> ['Homo sapiens'] - # - Homo sapiens; female --> ['Homo sapiens', 'female'] - # - Homo sapiens; female 63 --> ['Homo sapiens', 'female 63'] - # - Homo sapiens; female; age 40 --> ['Homo sapiens', 'female', 'age 40'] - # - Homo sapiens; gender: F; age: 61 --> ['Homo sapiens', 'gender: F', 'age: 61'] - # - Homo sapiens; gender: M; age: 68 --> ['Homo sapiens', 'gender: M', 'age: 68'] - # - Homo sapiens; hospitalized patient --> ['Homo sapiens', 'hospitalized patient'] - # - Homo sapiens; male --> ['Homo sapiens', 'male'] - # - Homo sapiens; male; 63 --> ['Homo sapiens', 'male', '63'] - # - Homo sapiens; male; age 29 --> ['Homo sapiens', 'male', 'age 29'] - # - Homo sapiens; symptomatic --> ['Homo sapiens', 'symptomatic'] - if len(GBQualifier_value_text_list) > 1: - host_sex = '' - if 'female' in GBQualifier_value_text_list[1]: - host_sex = 'female' - elif 'male' in GBQualifier_value_text_list[1]: - host_sex = 'male' - elif 'gender' in GBQualifier_value_text_list[1]: + + elif 'gender' in GBQualifier_value_text_list[1]: host_sex_one_lecter = GBQualifier_value_text_list[1].split(':')[-1].strip() if host_sex_one_lecter in ['F', 'M']: host_sex = 'female' if host_sex_one_lecter == 'F' else 'male' |