diff options
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 30 |
1 files changed, 13 insertions, 17 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 148a7e1..21ed3b2 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -37,8 +37,7 @@ if not os.path.exists(dir_metadata): tmp_list = [x.split('.')[0] for x in tmp_list] print(term, len(tmp_list)) - tmp_list=tmp_list - # tmp_list = tmp_list[0:2] # restricting to small run + #tmp_list = tmp_list[0:2] # restricting to small run id_set.update([x.split('.')[0] for x in tmp_list]) @@ -112,13 +111,13 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['sample']['sample_id'] = accession_version - info_for_yaml_dict['sample']['source_database_accession'] = "http://identifiers.org/insdc/"+accession_version+"#sequence" #accession is turned into resolvable URL/URI now + info_for_yaml_dict['sample']['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now # 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')]) + info_for_yaml_dict['submitter']['authors'] = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')] GBReference = GBSeq_references.find('GBReference') if GBReference is not None: @@ -126,7 +125,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBReference_journal is not None and GBReference_journal.text != 'Unpublished': if 'Submitted' in GBReference_journal.text: - info_for_yaml_dict['submitter']['submitter_name'] = GBReference_journal.text.split(')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_name'] = ["{}".format(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 @@ -146,8 +145,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if field_in_yaml == 'sequencing_coverage': # 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").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>')) + info_for_yaml_dict['technology'][field_in_yaml] = [ + float(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 @@ -162,8 +162,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) new_seq_tec_list.append(seq_tec) - for n, seq_tec in enumerate(new_seq_tec_list): - info_for_yaml_dict['technology'][field_in_yaml + ('' if n == 0 else str(n + 1))] = seq_tec + info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list] else: info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse @@ -210,17 +209,14 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa' if GBQualifier_value_text in term_to_uri_dict: - info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text] + 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', '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'] - elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab'] - info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat swab'] + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']] + elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab']: + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] elif GBQualifier_value_text in ['nasopharyngeal aspirate/throat swab']: - 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'] + info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] else: missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) elif GBQualifier_name_text == 'collection_date': |