From 1a1ba7504eff79bac6f8d7054abd418b734ae69c Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Mon, 6 Jul 2020 10:19:50 +0200 Subject: new terms in the sequencing_technology dictionary --- .../ncbi_sequencing_technology.csv | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'scripts/dict_ontology_standardization') diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv index 964cbf3..79c1269 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -33,3 +33,24 @@ ThermoFisher S5Plus,http://purl.obolibrary.org/obo/NCIT_C125894 Sanger dideoxy sequencing,http://purl.obolibrary.org/obo/NCIT_C19641 MGISEQ 2000,http://virtual-bh/MGISEQ2000 MGISEQ2000,http://virtual-bh/MGISEQ2000 +Illumina HiSeq X,http://www.ebi.ac.uk/efo/EFO_0008567 +ONT GridION X5,http://www.ebi.ac.uk/efo/EFO_0008633 +ONT PremethION,http://www.ebi.ac.uk/efo/EFO_0008634 +PacBio RS II,http://www.ebi.ac.uk/efo/EFO_0008631 +PacBio Sequel System,http://www.ebi.ac.uk/efo/EFO_0008630 +Illumina Genome Analyzer,http://www.ebi.ac.uk/efo/EFO_0004200 +Illumina Genome Analyzer II,http://www.ebi.ac.uk/efo/EFO_0004201 +Illumina Genome Analyzer IIx,http://www.ebi.ac.uk/efo/EFO_0004202 +454 GS 20 sequencer,http://www.ebi.ac.uk/efo/EFO_0004206 +454 GS FLX Titanium sequencer,http://www.ebi.ac.uk/efo/EFO_0004433 +454 GS FLX sequencer,http://www.ebi.ac.uk/efo/EFO_0004432 +454 GS Junior sequencer,http://www.ebi.ac.uk/efo/EFO_0004434 +454 GS sequencer,http://www.ebi.ac.uk/efo/EFO_0004431 +AB SOLiD 4 System,http://www.ebi.ac.uk/efo/EFO_0004438 +AB SOLiD 4hq System,http://www.ebi.ac.uk/efo/EFO_0004441 +AB SOLiD 5500,http://www.ebi.ac.uk/efo/EFO_0004440 +AB SOLiD 5500xl,http://www.ebi.ac.uk/efo/EFO_0004436 +AB SOLiD PI System,http://www.ebi.ac.uk/efo/EFO_0004437 +AB SOLiD System,http://www.ebi.ac.uk/efo/EFO_0004435 +AB SOLiD System 2.0,http://www.ebi.ac.uk/efo/EFO_0004442 +AB SOLiD System 3.0,http://www.ebi.ac.uk/efo/EFO_0004439 -- cgit v1.2.3 From 38a5b6d21d6bf631ade1b0875ca654331d50021a Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Mon, 6 Jul 2020 11:19:46 +0200 Subject: two more terms in the ncbi_sequencing_technology dictionary --- scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv | 2 ++ 1 file changed, 2 insertions(+) (limited to 'scripts/dict_ontology_standardization') diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv index 79c1269..59c4800 100644 --- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv +++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv @@ -13,12 +13,14 @@ Illumina NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566 NextSeq550,http://www.ebi.ac.uk/efo/EFO_0008566 NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566 Illumina MiniSeq,http://www.ebi.ac.uk/efo/EFO_0008636 +Illumina NovaSeq,http://www.ebi.ac.uk/efo/EFO_0008637 Illumina NovaSeq 6000,http://www.ebi.ac.uk/efo/EFO_0008637 Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632 Oxford Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632 ONT (Oxford Nanopore Technologies),http://purl.obolibrary.org/obo/NCIT_C146818 Oxford Nanopore Technology,http://purl.obolibrary.org/obo/NCIT_C146818 Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632 +Oxford Nanopore Sequencing,http://purl.obolibrary.org/obo/NCIT_C146818 MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632 MinION,http://www.ebi.ac.uk/efo/EFO_0008632 Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818 -- cgit v1.2.3 From 92639cf2616e02a798521e61598393d6d1aad5e3 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino Date: Mon, 6 Jul 2020 11:03:31 +0200 Subject: new terms in the ncbi_countries dictionary --- .../ncbi_countries.csv | 42 ++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'scripts/dict_ontology_standardization') diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index 204f7f2..ef8cbaa 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -284,6 +284,7 @@ USA:CA,http://www.wikidata.org/entity/Q99 USA: California,http://www.wikidata.org/entity/Q99 USA:California,http://www.wikidata.org/entity/Q99 "USA: CA, San Diego County",http://www.wikidata.org/entity/Q108143 +"USA: California, Monterey County",http://www.wikidata.org/entity/Q108072 USA: CO,http://www.wikidata.org/entity/Q1261 USA: CT,http://www.wikidata.org/entity/Q779 USA: Connecticut,http://www.wikidata.org/entity/Q779 @@ -301,8 +302,14 @@ USA: IN,http://www.wikidata.org/entity/Q1415 USA: KS,http://www.wikidata.org/entity/Q1558 USA: KY,http://www.wikidata.org/entity/Q1603 USA: LA,http://www.wikidata.org/entity/Q1588 +<<<<<<< HEAD USA:Los Angeles,http://www.wikidata.org/entity/Q65 "USA: New Orleans, LA",http://www.wikidata.org/entity/Q34404 +======= +"USA: SLIDELL, LA, LA",https://www.wikidata.org/wiki/Q988156 +"USA: Slidell, LA, LA",https://www.wikidata.org/wiki/Q988156 +"USA: New Orleans, LA",https://www.wikidata.org/wiki/Q34404 +>>>>>>> 67e5976... new terms in the ncbi_countries dictionary USA: MA,http://www.wikidata.org/entity/Q771 USA: Massachusetts,http://www.wikidata.org/entity/Q771 USA: MD,http://www.wikidata.org/entity/Q1391 @@ -336,6 +343,33 @@ USA: SC,http://www.wikidata.org/entity/Q1456 USA: South Carolina,http://www.wikidata.org/entity/Q1456 USA: SD,http://www.wikidata.org/entity/Q1211 "USA: Snohomish County, WA",http://www.wikidata.org/entity/Q110403 +"USA: Washington,Snohomish County",http://www.wikidata.org/entity/Q110403 +"USA: Washington, Snohomish County",http://www.wikidata.org/entity/Q110403 +"USA: Washington,Skagit County",http://www.wikidata.org/entity/Q113892 +"USA: Washington, Skagit County",http://www.wikidata.org/entity/Q113892 +"USA: Washington,Pierce County",http://www.wikidata.org/entity/Q156459 +"USA: Washington, Pierce County",http://www.wikidata.org/entity/Q156459 +"USA: Washington,Mason County",http://www.wikidata.org/entity/Q111904 +"USA: Washington, Mason County",http://www.wikidata.org/entity/Q111904 +"USA: Washington,Kittitas County",http://www.wikidata.org/entity/Q111540 +"USA: Washington,King County",http://www.wikidata.org/entity/Q108861 +"USA: Washington, King County",http://www.wikidata.org/entity/Q108861 +"USA: King County,WA",http://www.wikidata.org/entity/Q108861 +"USA: Washington,Jefferson County",http://www.wikidata.org/entity/Q384737 +"USA: Washington,Grant County",http://www.wikidata.org/entity/Q281681 +"USA: Washington, Grant County",http://www.wikidata.org/entity/Q281681 +"USA: Washington,Franklin County",http://www.wikidata.org/entity/Q118716 +"USA: Washington, Franklin County",http://www.wikidata.org/entity/Q118716 +"USA: Washington,Clark County",http://www.wikidata.org/entity/Q156287 +"USA: Washington,Benton County",http://www.wikidata.org/entity/Q156216 +"USA: Washington, Benton County",http://www.wikidata.org/entity/Q156216 +"USA: Washington,Asotin County",http://www.wikidata.org/entity/Q156295 +"USA: Washington, Asotin County",http://www.wikidata.org/entity/Q156295 +"USA: Washington,Adams County",http://www.wikidata.org/entity/Q156273 +"USA: Washington, Adams County",http://www.wikidata.org/entity/Q156273 +"USA: Washington, Spokane County",http://www.wikidata.org/entity/Q485276 +"USA: Washington, Douglas County",http://www.wikidata.org/entity/Q156220 +"USA: Washington, Cowlitz County",http://www.wikidata.org/entity/Q156276 USA: TN,http://www.wikidata.org/entity/Q1509 USA: TX,http://www.wikidata.org/entity/Q1439 USA: UT,http://www.wikidata.org/entity/Q829 @@ -344,9 +378,17 @@ USA: Virginia,http://www.wikidata.org/entity/Q1370 USA:Virginia,http://www.wikidata.org/entity/Q1370 USA: VT,http://www.wikidata.org/entity/Q16551 USA: WA,http://www.wikidata.org/entity/Q1223 +<<<<<<< HEAD USA: Washington,http://www.wikidata.org/entity/Q1223 USA: WI,http://www.wikidata.org/entity/Q1537 USA: Wisconsin,http://www.wikidata.org/entity/Q1537 +======= +"USA: Washington,Yakima County",http://www.wikidata.org/entity/Q156629 +"USA: Washington, Yakima County",http://www.wikidata.org/entity/Q156629 +"USA: Washington,Whatcom County",http://www.wikidata.org/entity/Q156623 +USA: WI,http://www.wikidata.org/entity/Q1537 +"USA: Dane County, Wisconsin",http://www.wikidata.org/entity/Q502200 +>>>>>>> 67e5976... new terms in the ncbi_countries dictionary USA: WV,http://www.wikidata.org/entity/Q1371 USA: WY,http://www.wikidata.org/entity/Q1214 Uzbekistan,http://www.wikidata.org/entity/Q265 -- cgit v1.2.3 From c8b12b4e2b7e2e51315fe738f8bb4e37cb78ae55 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Mon, 6 Jul 2020 15:22:45 +0200 Subject: fix ncbi_countries dictionary --- scripts/dict_ontology_standardization/ncbi_countries.csv | 9 --------- 1 file changed, 9 deletions(-) (limited to 'scripts/dict_ontology_standardization') diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv index ef8cbaa..4bea3ec 100644 --- a/scripts/dict_ontology_standardization/ncbi_countries.csv +++ b/scripts/dict_ontology_standardization/ncbi_countries.csv @@ -302,14 +302,9 @@ USA: IN,http://www.wikidata.org/entity/Q1415 USA: KS,http://www.wikidata.org/entity/Q1558 USA: KY,http://www.wikidata.org/entity/Q1603 USA: LA,http://www.wikidata.org/entity/Q1588 -<<<<<<< HEAD -USA:Los Angeles,http://www.wikidata.org/entity/Q65 -"USA: New Orleans, LA",http://www.wikidata.org/entity/Q34404 -======= "USA: SLIDELL, LA, LA",https://www.wikidata.org/wiki/Q988156 "USA: Slidell, LA, LA",https://www.wikidata.org/wiki/Q988156 "USA: New Orleans, LA",https://www.wikidata.org/wiki/Q34404 ->>>>>>> 67e5976... new terms in the ncbi_countries dictionary USA: MA,http://www.wikidata.org/entity/Q771 USA: Massachusetts,http://www.wikidata.org/entity/Q771 USA: MD,http://www.wikidata.org/entity/Q1391 @@ -378,17 +373,13 @@ USA: Virginia,http://www.wikidata.org/entity/Q1370 USA:Virginia,http://www.wikidata.org/entity/Q1370 USA: VT,http://www.wikidata.org/entity/Q16551 USA: WA,http://www.wikidata.org/entity/Q1223 -<<<<<<< HEAD USA: Washington,http://www.wikidata.org/entity/Q1223 USA: WI,http://www.wikidata.org/entity/Q1537 USA: Wisconsin,http://www.wikidata.org/entity/Q1537 -======= "USA: Washington,Yakima County",http://www.wikidata.org/entity/Q156629 "USA: Washington, Yakima County",http://www.wikidata.org/entity/Q156629 "USA: Washington,Whatcom County",http://www.wikidata.org/entity/Q156623 -USA: WI,http://www.wikidata.org/entity/Q1537 "USA: Dane County, Wisconsin",http://www.wikidata.org/entity/Q502200 ->>>>>>> 67e5976... new terms in the ncbi_countries dictionary USA: WV,http://www.wikidata.org/entity/Q1371 USA: WY,http://www.wikidata.org/entity/Q1214 Uzbekistan,http://www.wikidata.org/entity/Q265 -- cgit v1.2.3 From 9b1457763c08028179b0987d385d1fe879062b64 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Tue, 7 Jul 2020 22:07:35 +0200 Subject: if the technology is not found, the YAML file is not created; managed longer species strings --- scripts/create_sra_metadata/create_sra_metadata.py | 5 +- .../ncbi_host_species.csv | 1 + .../from_genbank_to_fasta_and_yaml.py | 114 +++++++++++---------- 3 files changed, 64 insertions(+), 56 deletions(-) (limited to 'scripts/dict_ontology_standardization') diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 470980e..ef0d119 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -197,7 +197,6 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if INSTRUMENT_MODEL in term_to_uri_dict: info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]] else: - info_for_yaml_dict['technology']['additional_technology_information'] = INSTRUMENT_MODEL missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL])) #else: # print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict) @@ -237,6 +236,10 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): info_for_yaml_dict['sample']['collection_date'] = '1970-01-01' info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing" + if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: + print(accession, ' - technology not found') + continue + with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw: json.dump(info_for_yaml_dict, fw, indent=2) diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv index bc6ac04..40572a3 100644 --- a/scripts/dict_ontology_standardization/ncbi_host_species.csv +++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv @@ -5,5 +5,6 @@ sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606 Mustela lutreola,http://purl.obolibrary.org/obo/NCBITaxon_9666 Manis javanica,http://purl.obolibrary.org/obo/NCBITaxon_9974 Felis catus,http://purl.obolibrary.org/obo/NCBITaxon_9685 +Felis catus; Domestic Shorthair,http://purl.obolibrary.org/obo/NCBITaxon_9685 Panthera tigris jacksoni,http://purl.obolibrary.org/obo/NCBITaxon_419130 Canis lupus familiaris,http://purl.obolibrary.org/obo/NCBITaxon_9615 diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 7edb1dc..44308ed 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -218,12 +218,12 @@ 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: - info_for_yaml_dict['technology']['additional_technology_information'] = seq_tec missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec])) new_seq_tec_list.append(seq_tec) - info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list] + if len(new_seq_tec_list) > 0: + 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 @@ -241,58 +241,62 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text if GBQualifier_name_text == 'host': - GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - - if GBQualifier_value_text_list[0] in term_to_uri_dict: - info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[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 - info_for_yaml_dict['host']['host_species'] = term_to_uri_dict['Canis lupus familiaris'] + if GBQualifier_value_text in term_to_uri_dict: + # Cases like 'Felis catus; Domestic Shorthair' + info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text] 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]: - 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' - - if host_sex in ['male', 'female']: - info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383" - 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]] + GBQualifier_value_text_list = GBQualifier_value_text.split('; ') + + if GBQualifier_value_text_list[0] in term_to_uri_dict: + info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[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 + info_for_yaml_dict['host']['host_species'] = term_to_uri_dict['Canis lupus familiaris'] else: - missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]])) - - # Host age - host_age = -1 - if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]): - host_age = int(GBQualifier_value_text_list[1].split(' ')[-1]) - elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]): - host_age = int(GBQualifier_value_text_list[2].split(' ')[-1]) - - if host_age > -1: - info_for_yaml_dict['host']['host_age'] = host_age - info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036' - elif len(GBQualifier_value_text_list) > 2: - missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]])) + 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]: + 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' + + if host_sex in ['male', 'female']: + info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383" + 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: + missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]])) + + # Host age + host_age = -1 + if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]): + host_age = int(GBQualifier_value_text_list[1].split(' ')[-1]) + elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]): + host_age = int(GBQualifier_value_text_list[2].split(' ')[-1]) + + if host_age > -1: + info_for_yaml_dict['host']['host_age'] = host_age + info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036' + elif len(GBQualifier_value_text_list) > 2: + missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]])) elif GBQualifier_name_text == 'collected_by': if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]): info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text @@ -365,9 +369,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1] - # Remove technology key if empty! - if (info_for_yaml_dict['technology']=={}): - del info_for_yaml_dict['technology'] + if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: + print(accession_version, ' - technology not found') + continue with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw: fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) -- cgit v1.2.3