diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/from_genbank_to_fasta_and_yaml.py | 16 |
1 files changed, 10 insertions, 6 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index a7c9dc2..0c410d7 100644 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -1,5 +1,5 @@ from Bio import Entrez -Entrez.email = 'andresguarahino@gmail.com' +Entrez.email = 'insert_your_email@gmail.com' import xml.etree.ElementTree as ET import yaml @@ -54,7 +54,7 @@ if not os.path.exists(dir_metadata_today): for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)): path_metadata_xxx_xml = os.path.join(dir_metadata_today, 'metadata_{}.xml'.format(i)) - print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xml)) + print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml)) with open(path_metadata_xxx_xml, 'w') as fw: fw.write( @@ -69,7 +69,11 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x with open(path_dict_xxx_csv) as f: for line in f: - term, uri = line.strip('\n').split(',') + if len(line.split(',')) > 2: + term, uri = line.strip('\n').split('",') + term = term.strip('"') + else: + term, uri = line.strip('\n').split(',') term_to_uri_dict[term] = uri @@ -78,7 +82,7 @@ species_to_taxid_dict = { } -if os.path.exists(dir_fasta_and_yaml_today): +if not os.path.exists(dir_fasta_and_yaml_today): os.makedirs(dir_fasta_and_yaml_today) for path_metadata_xxx_xml in [os.path.join(dir_metadata_today, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata_today) if name_metadata_xxx_xml.endswith('.xml')]: @@ -182,7 +186,7 @@ if os.path.exists(dir_fasta_and_yaml_today): if GBQualifier_value_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text] else: - if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab']: + if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab', 'np/op']: info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab'] info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab'] else: @@ -203,7 +207,7 @@ if os.path.exists(dir_fasta_and_yaml_today): info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text elif GBQualifier_name_text == 'db_xref': info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1]) - + with open(os.path.join(dir_fasta_and_yaml_today, '{}.fasta'.format(accession_version)), 'w') as fw: fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) |