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authorLLTommy2020-06-12 22:44:28 +0200
committerGitHub2020-06-12 22:44:28 +0200
commit9931e5d6ddf02c1f0f4a27e8321a37078e1c060d (patch)
treed342f22f5091e9a28f12ba0b7bd772bed97d770a /scripts
parenta8674b7e5c726994a102ea8c47d0e82c12e23d51 (diff)
parentf3d27f234b008a1faaeea428f5bd935ea3a438d2 (diff)
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Merge pull request #82 from AndreaGuarracino/patch-17
the script is more robust and verbose
Diffstat (limited to 'scripts')
-rw-r--r--scripts/dict_ontology_standardization/ncbi_host_species.csv6
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py435
2 files changed, 227 insertions, 214 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
new file mode 100644
index 0000000..0d2120c
--- /dev/null
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -0,0 +1,6 @@
+Homo 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
+Panthera tigris jacksoni,http://purl.obolibrary.org/obo/NCBITaxon_419130
+Canis lupus familiaris,http://purl.obolibrary.org/obo/NCBITaxon_9615
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 65adb00..87e99d4 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -123,18 +123,12 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
else:
term, uri = line.strip('\n').split(',')
+ if term in term_to_uri_dict:
+ print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
+ continue
+
term_to_uri_dict[term] = uri
-species_to_taxid_dict = {
- 'Homo 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',
- 'Panthera tigris jacksoni': 'http://purl.obolibrary.org/obo/NCBITaxon_419130',
- 'Canis lupus familiaris': 'http://purl.obolibrary.org/obo/NCBITaxon_9615'
-}
-
-
if not os.path.exists(dir_fasta_and_yaml):
os.makedirs(dir_fasta_and_yaml)
@@ -142,6 +136,7 @@ min_len_to_count = 27500
num_seq_with_len_ge_X_bp = 0
missing_value_list = []
+accession_with_errors_list = []
for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]:
tree = ET.parse(path_metadata_xxx_xml)
@@ -155,232 +150,244 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
print(accession_version, ' - sequence not found')
continue
- #print(path_metadata_xxx_xml, accession_version)
-
- # A general default-empty yaml could be read from the definitive one
- info_for_yaml_dict = {
- 'id': 'placeholder',
- 'host': {},
- 'sample': {},
- 'virus': {},
- 'technology': {},
- 'submitter': {}
- }
-
-
- 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
-
-
- # submitter info
- GBSeq_references = GBSeq.find('GBSeq_references')
- if GBSeq_references is not None:
- 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:
- 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'] = ["{}".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
-
-
- GBSeq_comment = GBSeq.find('GBSeq_comment')
- if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
- prefix_split_string = '##Genome-Assembly' if GBSeq_comment.text.startswith('##Genome-') else '##Assembly'
-
- GBSeq_comment_text = GBSeq_comment.text.split(
- '{}-Data-START## ; '.format(prefix_split_string)
- )[1].split(' ; {}-Data-END##'.format(prefix_split_string))[0]
-
- for info_to_check, field_in_yaml in zip(
- ['Assembly Method', 'Coverage', 'Sequencing Technology'],
- ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
- ):
- if info_to_check in GBSeq_comment_text:
- tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-
- 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>'))
- ]
- except ValueError:
- print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
- pass
- elif field_in_yaml == 'sample_sequencing_technology':
- new_seq_tec_list = []
- for seq_tec in tech_info_to_parse.split(';'):
- seq_tec = seq_tec.strip()
- if seq_tec in term_to_uri_dict:
- seq_tec = term_to_uri_dict[seq_tec]
- else:
- missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
+ try:
+ #print(path_metadata_xxx_xml, accession_version)
- new_seq_tec_list.append(seq_tec)
+ # A general default-empty yaml could be read from the definitive one
+ info_for_yaml_dict = {
+ 'id': 'placeholder',
+ 'host': {},
+ 'sample': {},
+ 'virus': {},
+ 'technology': {},
+ 'submitter': {}
+ }
- 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
+ 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
- for GBFeature in GBSeq.iter('GBFeature'):
- if GBFeature.find('GBFeature_key').text != 'source':
- continue
- for GBQualifier in GBFeature.iter('GBQualifier'):
- GBQualifier_value = GBQualifier.find('GBQualifier_value')
- if GBQualifier_value is None:
- continue
- GBQualifier_value_text = GBQualifier_value.text
-
- 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 species_to_taxid_dict:
- info_for_yaml_dict['host']['host_species'] = species_to_taxid_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'] = species_to_taxid_dict['Canis lupus familiaris']
- 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]]
- 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
- else:
- info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'isolation_source':
- if GBQualifier_value_text.upper() in term_to_uri_dict:
- GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'
-
- # Little cleaning
- GBQualifier_value_text = GBQualifier_value_text.strip("/'")
-
- 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.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal 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', 'nasopharyngeal swab and throat swab', 'nasal swab and 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'], term_to_uri_dict['throat swab']]
+ # submitter info
+ GBSeq_references = GBSeq.find('GBSeq_references')
+ if GBSeq_references is not None:
+ 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:
+ 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'] = ["{}".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:
- 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?
- date_to_write = GBQualifier_value_text
-
- if len(GBQualifier_value_text.split('-')) == 1:
- if int(GBQualifier_value_text) < 2020:
- date_to_write = "{}-12-15".format(GBQualifier_value_text)
+ info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text
+
+
+ GBSeq_comment = GBSeq.find('GBSeq_comment')
+ if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
+ prefix_split_string = '##Genome-Assembly' if GBSeq_comment.text.startswith('##Genome-') else '##Assembly'
+
+ GBSeq_comment_text = GBSeq_comment.text.split(
+ '{}-Data-START## ; '.format(prefix_split_string)
+ )[1].split(' ; {}-Data-END##'.format(prefix_split_string))[0]
+
+ for info_to_check, field_in_yaml in zip(
+ ['Assembly Method', 'Coverage', 'Sequencing Technology'],
+ ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
+ ):
+ if info_to_check in GBSeq_comment_text:
+ tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
+
+ 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>'))
+ ]
+ except ValueError:
+ print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
+ pass
+ elif field_in_yaml == 'sample_sequencing_technology':
+ new_seq_tec_list = []
+ for seq_tec in tech_info_to_parse.split(';'):
+ seq_tec = seq_tec.strip()
+ if seq_tec in term_to_uri_dict:
+ seq_tec = term_to_uri_dict[seq_tec]
+ else:
+ 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]
else:
- date_to_write = "{}-01-15".format(GBQualifier_value_text)
+ info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
- if 'additional_collection_information' in info_for_yaml_dict['sample']:
- info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+
+ for GBFeature in GBSeq.iter('GBFeature'):
+ if GBFeature.find('GBFeature_key').text != 'source':
+ continue
+
+ for GBQualifier in GBFeature.iter('GBQualifier'):
+ GBQualifier_value = GBQualifier.find('GBQualifier_value')
+ if GBQualifier_value is None:
+ continue
+ GBQualifier_value_text = GBQualifier_value.text
+
+ 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']
else:
- info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
- elif len(GBQualifier_value_text.split('-')) == 2:
- date_to_write += '-15'
-
- if 'additional_collection_information' in info_for_yaml_dict['sample']:
- info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+ 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
else:
- info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
- elif len(GBQualifier_value_text.split('-')) == 3:
- GBQualifier_value_text_list = GBQualifier_value_text.split('-')
+ info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'isolation_source':
+ if GBQualifier_value_text.upper() in term_to_uri_dict:
+ GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'
- if GBQualifier_value_text_list[1].isalpha():
- date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
+ # Little cleaning
+ GBQualifier_value_text = GBQualifier_value_text.strip("/'")
- info_for_yaml_dict['sample']['collection_date'] = date_to_write
- 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:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[GBQualifier_value_text]]
+ else:
+ if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal 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', 'nasopharyngeal swab and throat swab', 'nasal swab and 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'], 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':
+ # TO_DO: which format we will use?
+ date_to_write = GBQualifier_value_text
+
+ if len(GBQualifier_value_text.split('-')) == 1:
+ if int(GBQualifier_value_text) < 2020:
+ date_to_write = "{}-12-15".format(GBQualifier_value_text)
+ else:
+ date_to_write = "{}-01-15".format(GBQualifier_value_text)
- if GBQualifier_value_text in term_to_uri_dict:
- info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[GBQualifier_value_text]
- else:
- missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text]))
- elif GBQualifier_name_text == 'note':
- if 'additional_collection_information' in info_for_yaml_dict['sample']:
- info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text
- else:
- info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'isolate':
- info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
- elif GBQualifier_name_text == 'db_xref':
- info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
+ if 'additional_collection_information' in info_for_yaml_dict['sample']:
+ info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+ else:
+ info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+ elif len(GBQualifier_value_text.split('-')) == 2:
+ date_to_write += '-15'
+ if 'additional_collection_information' in info_for_yaml_dict['sample']:
+ info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+ else:
+ info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
+ elif len(GBQualifier_value_text.split('-')) == 3:
+ GBQualifier_value_text_list = GBQualifier_value_text.split('-')
- # Remove technology key if empty!
- if (info_for_yaml_dict['technology']=={}):
- del info_for_yaml_dict['technology']
+ if GBQualifier_value_text_list[1].isalpha():
+ date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
- 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()))
+ info_for_yaml_dict['sample']['collection_date'] = date_to_write
+ 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:
+ info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[GBQualifier_value_text]
+ else:
+ missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text]))
+ elif GBQualifier_name_text == 'note':
+ if 'additional_collection_information' in info_for_yaml_dict['sample']:
+ info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text
+ else:
+ info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'isolate':
+ info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
+ elif GBQualifier_name_text == 'db_xref':
+ info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
- with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw:
- json.dump(info_for_yaml_dict, fw, indent=2)
+ # Remove technology key if empty!
+ if (info_for_yaml_dict['technology']=={}):
+ del info_for_yaml_dict['technology']
- if(len(GBSeq_sequence.text) >= min_len_to_count):
- num_seq_with_len_ge_X_bp += 1
+ 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()))
+ with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw:
+ json.dump(info_for_yaml_dict, fw, indent=2)
+
+
+ if(len(GBSeq_sequence.text) >= min_len_to_count):
+ num_seq_with_len_ge_X_bp += 1
+ except:
+ print("Unexpected error for the ID {}: {}".format(accession_version, sys.exc_info()[0]))
+ accession_with_errors_list.append(accession_version)
+ continue
if len(missing_value_list) > 0:
- with open('missing_terms.tsv', 'w') as fw:
+ path_missing_terms_tsv = 'missing_terms.tsv'
+ print('Written missing terms in {}'.format(path_missing_terms_tsv))
+ with open(path_missing_terms_tsv, 'w') as fw:
fw.write('\n'.join(missing_value_list))
+if len(accession_with_errors_list) > 0:
+ path_accession_with_errors_tsv = 'accession_with_errors.tsv'
+ print('Written the accession with errors in {}'.format(path_accession_with_errors_tsv))
+ with open(path_accession_with_errors_tsv, 'w') as fw:
+ fw.write('\n'.join(accession_with_errors_list))
+
print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))