diff options
| -rw-r--r-- | scripts/dict_ontology_standardization/ncbi_speciesman_source.csv | 1 | ||||
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 32 | ||||
| -rw-r--r-- | scripts/sequences.acc | 227 |
3 files changed, 248 insertions, 12 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv index 8278c90..f5aeaae 100644 --- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv +++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv @@ -24,3 +24,4 @@ aspirate,http://purl.obolibrary.org/obo/NCIT_C13347 stool,http://purl.obolibrary.org/obo/NCIT_C13234 serum,http://purl.obolibrary.org/obo/NCIT_C13325 saliva,http://purl.obolibrary.org/obo/NCIT_C13275 +nasal swab,http://purl.obolibrary.org/obo/NCIT_C132119 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= GBReference.find('GBReference_journal') + + if GBReference_journal is not None and GBReference_journal.text != 'Unpublished': + if 'Submitted' in GBReference_journal.text: + info_for_yaml_dict['submitter']['submitter_name'] = GBReference_journal.text.split(')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 diff --git a/scripts/sequences.acc b/scripts/sequences.acc index 0ad0878..a99c4e6 100644 --- a/scripts/sequences.acc +++ b/scripts/sequences.acc @@ -1,4 +1,231 @@ NC_045512 +MT370516 +MT370517 +MT370518 +MT370831 +MT370832 +MT370833 +MT370834 +MT370835 +MT370836 +MT370837 +MT370838 +MT370839 +MT370840 +MT370841 +MT370842 +MT370843 +MT370844 +MT370845 +MT370846 +MT370847 +MT370848 +MT370849 +MT370850 +MT370851 +MT370852 +MT370853 +MT370854 +MT370855 +MT370856 +MT370857 +MT370858 +MT370859 +MT370860 +MT370861 +MT370862 +MT370863 +MT370864 +MT370865 +MT370866 +MT370867 +MT370868 +MT370869 +MT370870 +MT370871 +MT370872 +MT370873 +MT370874 +MT370875 +MT370876 +MT370877 +MT370878 +MT370879 +MT370880 +MT370881 +MT370882 +MT370883 +MT370884 +MT370885 +MT370886 +MT370887 +MT370888 +MT370889 +MT370890 +MT370891 +MT370892 +MT370893 +MT370894 +MT370895 +MT370896 +MT370897 +MT370898 +MT370899 +MT370900 +MT370901 +MT370902 +MT370903 +MT370904 +MT370905 +MT370906 +MT370907 +MT370908 +MT370909 +MT370910 +MT370911 +MT370912 +MT370913 +MT370914 +MT370915 +MT370916 +MT370917 +MT370918 +MT370919 +MT370920 +MT370921 +MT370922 +MT370923 +MT370924 +MT370925 +MT370926 +MT370927 +MT370928 +MT370929 +MT370930 +MT370931 +MT370932 +MT370933 +MT370934 +MT370935 +MT370936 +MT370937 +MT370938 +MT370939 +MT370940 +MT370941 +MT370942 +MT370943 +MT370944 +MT370945 +MT370946 +MT370947 +MT370948 +MT370949 +MT370950 +MT370951 +MT370952 +MT370953 +MT370954 +MT370955 +MT370956 +MT370957 +MT370958 +MT370959 +MT370960 +MT370961 +MT370962 +MT370963 +MT370964 +MT370965 +MT370966 +MT370967 +MT370968 +MT370969 +MT370970 +MT370971 +MT370972 +MT370973 +MT370974 +MT370975 +MT370976 +MT370977 +MT370978 +MT370979 +MT370980 +MT370981 +MT370982 +MT370983 +MT370984 +MT370985 +MT370986 +MT370987 +MT370988 +MT370989 +MT370990 +MT370991 +MT370992 +MT370993 +MT370994 +MT370995 +MT370996 +MT370997 +MT370998 +MT370999 +MT371000 +MT371001 +MT371002 +MT371003 +MT371004 +MT371005 +MT371006 +MT371007 +MT371008 +MT371009 +MT371010 +MT371011 +MT371012 +MT371013 +MT371014 +MT371015 +MT371016 +MT371017 +MT371018 +MT371019 +MT371020 +MT371021 +MT371022 +MT371023 +MT371024 +MT371025 +MT371026 +MT371027 +MT371028 +MT371029 +MT371030 +MT371031 +MT371032 +MT371033 +MT371034 +MT371035 +MT371036 +MT371037 +MT371038 +MT371047 +MT371048 +MT371049 +MT371050 +MT371568 +MT371569 +MT371570 +MT371571 +MT371572 +MT371573 +MT371574 +MT372480 +MT372481 +MT372482 +MT372483 +LC542976 LC542809 MT114412 MT114413 |