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authorPjotr Prins2021-01-02 12:06:08 +0000
committerPjotr Prins2021-01-02 12:06:08 +0000
commit6fd44b33eec7e72da5578ddef88a3ad18576bc1f (patch)
treec62f6bf14210dbacb3d7a0631c0410393ff9d8b3
parenta029c2329e748874bee88317e44d3f47547f71d8 (diff)
downloadbh20-seq-resource-6fd44b33eec7e72da5578ddef88a3ad18576bc1f.tar.gz
bh20-seq-resource-6fd44b33eec7e72da5578ddef88a3ad18576bc1f.tar.lz
bh20-seq-resource-6fd44b33eec7e72da5578ddef88a3ad18576bc1f.zip
transform-genbank-xml2yamlfa.py rewrite
-rw-r--r--workflows/pull-data/genbank/README.md2
-rw-r--r--workflows/pull-data/genbank/genbank.py339
-rwxr-xr-xworkflows/pull-data/genbank/transform-genbank-xml2yamlfa.py383
-rwxr-xr-xworkflows/pull-data/genbank/update-from-genbank.py1
4 files changed, 403 insertions, 322 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
index 5597234..b5bac84 100644
--- a/workflows/pull-data/genbank/README.md
+++ b/workflows/pull-data/genbank/README.md
@@ -8,7 +8,7 @@
# --- fetch XML
python3 update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank
# --- Transform to YAML and FASTA
-transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq
+python3 transform-genbank-xml2yamlfa --out ~/tmp/pubseq file(s)
```
# TODO
diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py
new file mode 100644
index 0000000..7ce3913
--- /dev/null
+++ b/workflows/pull-data/genbank/genbank.py
@@ -0,0 +1,339 @@
+# Genbank XML parser
+
+import os
+import sys
+import xml.etree.ElementTree as ET
+
+class GBError(Exception):
+ pass
+
+def get_metadata(id, gb):
+ return True,None
+
+def get_sequence(id, gbseq):
+ seq = None
+ count = 0
+ for gbseq_sequence in gbseq.findall('./GBSeq_sequence'):
+ count += 1
+ if count > 1:
+ raise GBError(f"Expected one sequence for {id}")
+ seq = gbseq_sequence.text.upper()
+ print(f"SEQ: size={len(seq)}",seq[0:30])
+ if len(seq) < 20_000:
+ raise GBError(f"Sequence too short")
+ return seq
+
+min_len_to_count = 15000
+num_seq_with_len_ge_X_bp = 0
+
+missing_value_list = []
+not_created_accession_dict = {}
+accession_with_errors_list = []
+if None:
+
+ tree = ET.parse(path_metadata_xxx_xml)
+ GBSet = tree.getroot()
+
+ for GBSeq in GBSet:
+ accession_version = GBSeq.find('GBSeq_accession-version').text
+
+ GBSeq_sequence = GBSeq.find('GBSeq_sequence')
+ if GBSeq_sequence is None:
+ print(accession_version, ' - sequence not found')
+ continue
+
+ try:
+ # 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:
+ author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
+ if len(author_list) > 0:
+ info_for_yaml_dict['submitter']['authors'] = author_list
+
+ 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
+
+ # This script download and prepare data and metadata for assemblies samples
+ info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628'
+
+ 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'],
+ ['alignment_protocol', '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.replace('(average)', '').replace("reads/nt", '').
+ replace('(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 field_to_term_to_uri_dict['ncbi_sequencing_technology']:
+ seq_tec = field_to_term_to_uri_dict['ncbi_sequencing_technology'][seq_tec]
+ new_seq_tec_list.append(seq_tec)
+ else:
+ missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
+
+ 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
+
+
+ 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 = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female
+ if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']:
+ # Cases like 'Felis catus; Domestic Shorthair'
+ info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text]
+ else:
+ GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
+
+ if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']:
+ info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][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'] = field_to_term_to_uri_dict['ncbi_host_species']['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 field_to_term_to_uri_dict['ncbi_host_health_status']:
+ info_for_yaml_dict['host']['host_health_status'] = field_to_term_to_uri_dict['ncbi_host_health_status'][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 >= 0 and host_age < 110:
+ 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 field_to_term_to_uri_dict['ncbi_speciesman_source']:
+ 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 field_to_term_to_uri_dict['ncbi_speciesman_source']:
+ info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]]
+ else:
+ if GBQualifier_value_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']]
+ elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']:
+ info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
+ elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
+ elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
+ elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal 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 '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 = parse(GBQualifier_value_text).strftime('%Y-%m') + '-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('-')
+
+ if GBQualifier_value_text_list[1].isalpha():
+ date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
+
+ info_for_yaml_dict['sample']['collection_date'] = date_to_write
+ elif GBQualifier_name_text in ['lat_lon', 'country']:
+ if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text:
+ GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':')
+
+ if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_countries']:
+ info_for_yaml_dict['sample']['collection_location'] = field_to_term_to_uri_dict['ncbi_countries'][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]
+
+ # Check if mandatory fields are missing
+ if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
+ # print(accession_version, ' - technology not found')
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('sample_sequencing_technology not found')
+
+ if 'collection_location' not in info_for_yaml_dict['sample']:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('collection_location not found')
+
+ if 'collection_date' not in info_for_yaml_dict['sample']:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('collection_date not found')
+ else:
+ year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')]
+
+ collection_date_in_yaml = datetime(year, month, day)
+ if collection_date_in_yaml < min_acceptable_collection_date:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('collection_date too early')
+
+ if 'authors' not in info_for_yaml_dict['submitter']:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('authors not found')
+
+ if 'host_species' not in info_for_yaml_dict['host']:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('host_species not found')
+
+ if len(GBSeq_sequence.text) < min_len_to_count:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('sequence shorter than {} bp'.format(min_len_to_count))
+
+ if accession_version not in not_created_accession_dict:
+ 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)
+ 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:
+ path_missing_terms_tsv = 'missing_terms.genbank.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.genbank.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))
+
+if len(not_created_accession_dict) > 0:
+ path_not_created_accession_tsv = 'not_created_accession.genbank.tsv'
+ print('Written not created accession in {}'.format(path_not_created_accession_tsv))
+ with open(path_not_created_accession_tsv, 'w') as fw:
+ fw.write('\n'.join(['\t'.join([accession_version, ','.join(missing_info_list)]) for accession_version, missing_info_list in not_created_accession_dict.items()]))
+
+print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))
diff --git a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
index 8b970b6..c4e3eba 100755
--- a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
+++ b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
@@ -1,326 +1,67 @@
#!/usr/bin/env python3
#
# Create a single YAML/FASTA from genbank XML
-
+#
+# transform-genbank-xml2yamlfa --out ~/tmp/pubseq file(s)
+#
+# Also writes a validation file in the outdir named state.json
+#
+# Where --in can be a file or a directory
# ----------------------------------------------------------------------
-"""
-Generate metadata (YAML) and FASTA files for each accession
-"""
-
-if not os.path.exists(dir_fasta_and_yaml):
- os.makedirs(dir_fasta_and_yaml)
-
-min_len_to_count = 15000
-num_seq_with_len_ge_X_bp = 0
-
-missing_value_list = []
-not_created_accession_dict = {}
-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)
- GBSet = tree.getroot()
-
- for GBSeq in GBSet:
- accession_version = GBSeq.find('GBSeq_accession-version').text
-
- GBSeq_sequence = GBSeq.find('GBSeq_sequence')
- if GBSeq_sequence is None:
- print(accession_version, ' - sequence not found')
- continue
-
- try:
- # 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:
- author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
- if len(author_list) > 0:
- info_for_yaml_dict['submitter']['authors'] = author_list
-
- 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
-
- # This script download and prepare data and metadata for assemblies samples
- info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628'
-
- 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'],
- ['alignment_protocol', '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.replace('(average)', '').replace("reads/nt", '').
- replace('(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 field_to_term_to_uri_dict['ncbi_sequencing_technology']:
- seq_tec = field_to_term_to_uri_dict['ncbi_sequencing_technology'][seq_tec]
- new_seq_tec_list.append(seq_tec)
- else:
- missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
-
- 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
-
-
- 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 = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female
- if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']:
- # Cases like 'Felis catus; Domestic Shorthair'
- info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text]
- else:
- GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
-
- if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']:
- info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][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'] = field_to_term_to_uri_dict['ncbi_host_species']['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 field_to_term_to_uri_dict['ncbi_host_health_status']:
- info_for_yaml_dict['host']['host_health_status'] = field_to_term_to_uri_dict['ncbi_host_health_status'][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 >= 0 and host_age < 110:
- 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 field_to_term_to_uri_dict['ncbi_speciesman_source']:
- 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 field_to_term_to_uri_dict['ncbi_speciesman_source']:
- info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]]
- else:
- if GBQualifier_value_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']:
- info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']]
- elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']:
- info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
- elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']:
- info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
- elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']:
- info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
- elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
- info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal 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 '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 = parse(GBQualifier_value_text).strftime('%Y-%m') + '-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('-')
-
- if GBQualifier_value_text_list[1].isalpha():
- date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
-
- info_for_yaml_dict['sample']['collection_date'] = date_to_write
- elif GBQualifier_name_text in ['lat_lon', 'country']:
- if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text:
- GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':')
-
- if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_countries']:
- info_for_yaml_dict['sample']['collection_location'] = field_to_term_to_uri_dict['ncbi_countries'][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]
-
- # Check if mandatory fields are missing
- if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
- # print(accession_version, ' - technology not found')
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('sample_sequencing_technology not found')
-
- if 'collection_location' not in info_for_yaml_dict['sample']:
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('collection_location not found')
-
- if 'collection_date' not in info_for_yaml_dict['sample']:
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('collection_date not found')
- else:
- year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')]
-
- collection_date_in_yaml = datetime(year, month, day)
- if collection_date_in_yaml < min_acceptable_collection_date:
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('collection_date too early')
-
- if 'authors' not in info_for_yaml_dict['submitter']:
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('authors not found')
-
- if 'host_species' not in info_for_yaml_dict['host']:
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('host_species not found')
-
- if len(GBSeq_sequence.text) < min_len_to_count:
- if accession_version not in not_created_accession_dict:
- not_created_accession_dict[accession_version] = []
- not_created_accession_dict[accession_version].append('sequence shorter than {} bp'.format(min_len_to_count))
-
- if accession_version not in not_created_accession_dict:
- 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)
- 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:
- path_missing_terms_tsv = 'missing_terms.genbank.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.genbank.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))
-
-if len(not_created_accession_dict) > 0:
- path_not_created_accession_tsv = 'not_created_accession.genbank.tsv'
- print('Written not created accession in {}'.format(path_not_created_accession_tsv))
- with open(path_not_created_accession_tsv, 'w') as fw:
- fw.write('\n'.join(['\t'.join([accession_version, ','.join(missing_info_list)]) for accession_version, missing_info_list in not_created_accession_dict.items()]))
-print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))
+# See also directory .guix-run and README.md
+
+import argparse
+import gzip
+import os
+import sys
+import types
+import xml.etree.ElementTree as ET
+from utils import chunks
+import genbank
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--out', type=str, help='Directory to write to',
+required=True)
+parser.add_argument('files', nargs='+', help='file(s)')
+args = parser.parse_args()
+
+dir = args.out
+if not os.path.exists(dir):
+ raise Exception(f"Directory {dir} does not exist")
+
+states = {}
+
+for xmlfn in args.files:
+ print(f"--- Reading {xmlfn}")
+ with gzip.open(xmlfn, 'r') as f:
+ xml = f.read().decode()
+ tree = ET.fromstring(xml)
+ for gb in tree.findall('./GBSeq'):
+ valid = None
+ error = None
+ id = gb.find("GBSeq_locus").text
+ basename = dir+"/"+id
+ print(f" parsing {id}")
+ try:
+ valid,meta = genbank.get_metadata(id,gb)
+ if valid:
+ fa = basename+".fa"
+ seq = genbank.get_sequence(id,gb)
+ print(f" writing {fa}")
+ with open(fa,"w") as f2:
+ f2.write(f"> {id}\n")
+ f2.write(seq)
+ # print(seq)
+ except genbank.GBError as e:
+ print(f"OS error: {e}")
+ valid = False
+ error = str(e)
+ state = {}
+ if not valid:
+ state['valid'] = False
+ if error:
+ state['error'] = error
+ states[id] = state
+
+print(states)
diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/update-from-genbank.py
index 3faea39..dca5563 100755
--- a/workflows/pull-data/genbank/update-from-genbank.py
+++ b/workflows/pull-data/genbank/update-from-genbank.py
@@ -22,6 +22,7 @@ parser = argparse.ArgumentParser()
parser.add_argument('--max', type=int, help='Max queries', required=False)
parser.add_argument('--ids', type=str, help='File with ids to fetch, 1 id per line', required=True)
parser.add_argument('--out', type=str, help='Directory to write to', required=True)
+
args = parser.parse_args()
ids = set()