diff options
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 32 |
1 files changed, 20 insertions, 12 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index f76cb29..5257bd1 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -110,9 +110,26 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) 'submitter': {} } + info_for_yaml_dict['sample']['sample_id'] = accession_version info_for_yaml_dict['sample']['source_database_accession'] = accession_version - info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')]) + + + # submitter info + GBSeq_references = GBSeq.find('GBSeq_references') + if GBSeq_references is not None: + info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq_references.iter('GBAuthor')]) + + GBReference = GBSeq_references.find('GBReference') + if GBReference is not None: + GBReference_journal = GBReference.find('GBReference_journal') + + if GBReference_journal is not None and GBReference_journal.text != 'Unpublished': + if 'Submitted' in GBReference_journal.text: + info_for_yaml_dict['submitter']['submitter_name'] = GBReference_journal.text.split(') ')[1].split(',')[0].strip() + info_for_yaml_dict['submitter']['submitter_address'] = ','.join(GBReference_journal.text.split(') ')[1].split(',')[1:]).strip() + else: + info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text GBSeq_comment = GBSeq.find('GBSeq_comment') @@ -130,7 +147,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) # A regular expression would be better! try: info_for_yaml_dict['technology'][field_in_yaml] = float( - tech_info_to_parse.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>')) + tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>')) except ValueError: print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse) pass @@ -141,7 +158,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if seq_tec in term_to_uri_dict: seq_tec = term_to_uri_dict[seq_tec] else: - #print(accession_version, 'missing sample_sequencing_technology:', seq_tec) missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec])) new_seq_tec_list.append(seq_tec) @@ -152,8 +168,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse - #term_to_uri_dict - for GBFeature in GBSeq.iter('GBFeature'): if GBFeature.find('GBFeature_key').text != 'source': continue @@ -169,8 +183,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_name_text == 'host': GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - #info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] # Removed - if GBQualifier_value_text_list[0] in species_to_taxid_dict: info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]] @@ -183,7 +195,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) elif GBQualifier_value_text_list[1] in term_to_uri_dict: info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[GBQualifier_value_text_list[1]] else: - #print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text_list[1]) missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text_list[1]])) if 'age' in GBQualifier_value_text: @@ -211,7 +222,6 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal aspirate'] info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat swab'] else: - #print(accession_version, 'missing specimen_source:', GBQualifier_value_text) missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) elif GBQualifier_name_text == 'collection_date': # TO_DO: which format we will use? @@ -219,12 +229,10 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) elif GBQualifier_name_text in ['lat_lon', 'country']: if GBQualifier_value_text == 'Hong Kong': GBQualifier_value_text = 'China: Hong Kong' - - + if GBQualifier_value_text in term_to_uri_dict: GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text] else: - #print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text) missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text])) info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text |