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authorLLTommy2020-06-24 08:45:07 +0200
committerGitHub2020-06-24 08:45:07 +0200
commit73ac4b91a44779a54c77e29ba1e8ee52291e390e (patch)
treeb90d3576b3f54e19c0d07156f7b69abb0e12fba4
parentb188fa4d896e1159ae424ab1c9bcfb21eb8ac67b (diff)
parent2d822c049f2b7f3e62a3ac4c19c827428b6f73e2 (diff)
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Merge pull request #87 from AndreaGuarracino/patch-20
added script to crete metadata for SRA data; new dictionary entries; little directory changes
-rw-r--r--scripts/README.md6
-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv4
-rw-r--r--scripts/dict_ontology_standardization/ncbi_host_species.csv1
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv7
-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py (renamed from scripts/from_genbank_to_fasta_and_yaml.py)12
-rw-r--r--scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gzbin0 -> 3227724 bytes
-rw-r--r--scripts/download_sra_data/download_sra_data.py232
-rw-r--r--scripts/sequences.acc1731
8 files changed, 257 insertions, 1736 deletions
diff --git a/scripts/README.md b/scripts/README.md
new file mode 100644
index 0000000..a3ed1b6
--- /dev/null
+++ b/scripts/README.md
@@ -0,0 +1,6 @@
+### Instructions for download and/or prepare the data and/ or the metadata
+
+Just go into the `download_genbank_data` or `download_sra_data` directory and execute the python3 script inside.
+
+- `download_genbank_data/from_genbank_to_fasta_and_yaml.py` downloads the data and the matadata, preparing the FASTA and the YAML files;
+- `download_sra_data/download_sra_data.py` creates the metadata in the form of YAML files from the SraExperimentPackage.XXX.xml.gz file in the same directory.
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 85d4e8a..204f7f2 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -239,6 +239,7 @@ Solomon Islands,http://www.wikidata.org/entity/Q685
Somalia,http://www.wikidata.org/entity/Q1045
South Africa,http://www.wikidata.org/entity/Q258
South Africa: KwaZulu-Natal,http://www.wikidata.org/entity/Q81725
+South Africa: KZN,http://www.wikidata.org/entity/Q81725
South African Republic,http://www.wikidata.org/entity/Q550374
South Korea,http://www.wikidata.org/entity/Q884
South Sudan,http://www.wikidata.org/entity/Q958
@@ -279,6 +280,7 @@ USA: AR,http://www.wikidata.org/entity/Q1612
USA: AZ,http://www.wikidata.org/entity/Q816
USA: Arizona,http://www.wikidata.org/entity/Q816
USA: CA,http://www.wikidata.org/entity/Q99
+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
@@ -299,6 +301,7 @@ 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
+USA:Los Angeles,http://www.wikidata.org/entity/Q65
"USA: New Orleans, LA",http://www.wikidata.org/entity/Q34404
USA: MA,http://www.wikidata.org/entity/Q771
USA: Massachusetts,http://www.wikidata.org/entity/Q771
@@ -330,6 +333,7 @@ USA: PA,http://www.wikidata.org/entity/Q1400
USA: RI,http://www.wikidata.org/entity/Q1387
"USA: San Francisco, CA",http://www.wikidata.org/entity/Q62
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: TN,http://www.wikidata.org/entity/Q1509
diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
index 102d458..bc6ac04 100644
--- a/scripts/dict_ontology_standardization/ncbi_host_species.csv
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -1,6 +1,7 @@
Homo sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606
human,http://purl.obolibrary.org/obo/NCBITaxon_9606
Human,http://purl.obolibrary.org/obo/NCBITaxon_9606
+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
diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
index 110e90b..964cbf3 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -1,3 +1,9 @@
+Illumina HiSeq 1000,http://www.ebi.ac.uk/efo/EFO_0004204
+Illumina HiSeq 2000,http://www.ebi.ac.uk/efo/EFO_0004203
+Illumina HiSeq 2500,http://www.ebi.ac.uk/efo/EFO_0008565
+Illumina HiSeq 3000,http://www.ebi.ac.uk/efo/EFO_0008564
+Illumina HiSeq 4000,http://www.ebi.ac.uk/efo/EFO_0008563
+Illumina iSeq 100,http://www.ebi.ac.uk/efo/EFO_0008635
Illumian NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
Illumina NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
NextSeq500,http://www.ebi.ac.uk/efo/EFO_0009173
@@ -14,6 +20,7 @@ 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
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
Illumina MiSeq,http://www.ebi.ac.uk/efo/EFO_0004205
Illumina,http://purl.obolibrary.org/obo/OBI_0000759
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index 87e99d4..d76f56b 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -22,7 +22,7 @@ num_ids_for_request = 100
dir_metadata = 'metadata_from_nuccore'
dir_fasta_and_yaml = 'fasta_and_yaml'
-dir_dict_ontology_standardization = 'dict_ontology_standardization/'
+dir_dict_ontology_standardization = '../dict_ontology_standardization/'
today_date = date.today().strftime("%Y.%m.%d")
path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
@@ -305,12 +305,14 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
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']:
+ if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and 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']:
+ 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']:
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']]
+ elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']]
+ elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['oropharyngeal swab']]
else:
missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text]))
elif GBQualifier_name_text == 'collection_date':
diff --git a/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz b/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
new file mode 100644
index 0000000..f9cd995
--- /dev/null
+++ b/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
Binary files differ
diff --git a/scripts/download_sra_data/download_sra_data.py b/scripts/download_sra_data/download_sra_data.py
new file mode 100644
index 0000000..9145a43
--- /dev/null
+++ b/scripts/download_sra_data/download_sra_data.py
@@ -0,0 +1,232 @@
+#!/usr/bin/env python3
+
+import os
+from dateutil.parser import parse
+import xml.etree.ElementTree as ET
+import json
+import gzip
+
+dir_yaml = 'yaml'
+
+date = '2020.06.08'
+
+# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) -> Send to -> File -> Full XML -> Create File
+path_sra_metadata_xml = 'SraExperimentPackage.{}.xml.gz'.format(date)
+
+dir_dict_ontology_standardization = '../dict_ontology_standardization/'
+path_sra_study_accessions_txt = 'SRAStudyAccessions.{}.txt'.format(date)
+
+term_to_uri_dict = {}
+
+for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]:
+ print('Read {}'.format(path_dict_xxx_csv))
+
+ with open(path_dict_xxx_csv, 'r') as f:
+ for line in f:
+ if len(line.split(',')) > 2:
+ term, uri = line.strip('\n').split('",')
+ term = term.strip('"')
+ else:
+ term, uri = line.strip('\n').split(',')
+
+ term_to_uri_dict[term] = uri
+
+def is_integer(string_to_check):
+ try:
+ int(string_to_check)
+ return True
+ except ValueError:
+ return False
+
+if not os.path.exists(dir_yaml):
+ os.makedirs(dir_yaml)
+
+sra_metadata_xml_file = gzip.open(path_sra_metadata_xml, 'r')
+tree = ET.parse(sra_metadata_xml_file)
+sra_metadata_xml_file.close()
+
+EXPERIMENT_PACKAGE_SET = tree.getroot()
+
+missing_value_list = []
+
+run_accession_set = set()
+run_accession_to_downloadble_file_url_dict = {}
+
+for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
+ #print(i, EXPERIMENT_PACKAGE)
+
+ # A general default-empty yaml could be read from the definitive one
+ info_for_yaml_dict = {
+ 'id': 'placeholder',
+ 'host': {},
+ 'sample': {},
+ 'virus': {},
+ 'technology': {},
+ 'submitter': {}
+ }
+
+ RUN_SET = EXPERIMENT_PACKAGE.find('RUN_SET')
+ RUN = RUN_SET.find('RUN')
+ accession = RUN.attrib['accession']
+ run_accession_set.add(accession)
+ #print(accession)
+
+ info_for_yaml_dict['sample']['sample_id'] = accession
+
+ SRAFiles = RUN.find('SRAFiles')
+ if SRAFiles is not None:
+ url = SRAFiles.find('SRAFile').attrib['url']
+ if 'sra-download.ncbi.nlm.nih.gov' in url:
+ run_accession_to_downloadble_file_url_dict[accession] = url
+
+
+ SAMPLE = EXPERIMENT_PACKAGE.find('SAMPLE')
+ SAMPLE_ATTRIBUTE_list = SAMPLE.iter('SAMPLE_ATTRIBUTE')
+
+ for SAMPLE_ATTRIBUTE in SAMPLE_ATTRIBUTE_list:
+ VALUE = SAMPLE_ATTRIBUTE.find('VALUE')
+ if VALUE is not None:
+ TAG_text = SAMPLE_ATTRIBUTE.find('TAG').text
+ VALUE_text = VALUE.text
+
+ if TAG_text in ['host', 'host scientific name']:
+ if VALUE_text in term_to_uri_dict:
+ info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[VALUE_text]
+ else:
+ missing_value_list.append('\t'.join([accession, 'host_species', VALUE_text]))
+ elif TAG_text in ['host_health_status', 'host health state']:
+ if VALUE_text in term_to_uri_dict:
+ info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[VALUE_text]
+ elif VALUE_text.strip("'") not in ['missing', 'not collected', 'not provided']:
+ missing_value_list.append('\t'.join([accession, 'host_health_status', VALUE_text]))
+ elif TAG_text in ['strain', 'isolate']:
+ if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown']:
+ if 'virus_strain' not in info_for_yaml_dict:
+ info_for_yaml_dict['virus']['virus_strain'] = VALUE_text
+ else:
+ info_for_yaml_dict['virus']['virus_strain'] += '; ' + VALUE_text
+ elif TAG_text in ['isolation_source', 'isolation source host-associated']:
+ if VALUE_text in term_to_uri_dict:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]]
+ else:
+ if VALUE_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']]
+ elif 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']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']]
+ elif VALUE_text.lower() in ['nasal swab and throat swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']]
+ elif VALUE_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['oropharyngeal swab']]
+ elif VALUE_text.strip("'") not in ['missing', 'not collected', 'unknown', 'not provided', 'not applicable', 'N/A']:
+ missing_value_list.append('\t'.join([accession, 'specimen_source', VALUE_text]))
+ elif TAG_text in ['host_sex', 'host sex']:
+ if VALUE_text.lower() not in ['missing', 'not provided']:
+ if VALUE_text in ['male', 'female']:
+ info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if VALUE_text == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383"
+ else:
+ missing_value_list.append('\t'.join([accession, 'host_sex', VALUE_text]))
+ elif TAG_text in ['host_age', 'host age']:
+ if is_integer(VALUE_text):
+ info_for_yaml_dict['host']['host_age'] = VALUE_text
+ info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
+ elif TAG_text == 'collected_by':
+ if VALUE_text.lower() not in ['not available', 'missing']:
+ name = VALUE_text in ['Dr. Susie Bartlett', 'Ahmed Babiker', 'Aisi Fu', 'Brandi Williamson', 'George Taiaroa', 'Natacha Ogando', 'Tim Dalebout', 'ykut Ozdarendeli']
+
+ info_for_yaml_dict['sample']['collector_name' if name else 'collecting_institution'] = VALUE_text
+ elif TAG_text == 'collecting institution':
+ if VALUE_text.lower() not in ['not provided', 'na']:
+ info_for_yaml_dict['sample']['collecting_institution'] = VALUE_text
+ elif TAG_text in ['collection_date', 'collection date']:
+ if VALUE_text.lower() not in ['not applicable', 'missing', 'na']:
+ date_to_write = VALUE_text
+ date_is_estimated = True
+
+ VALUE_text_list = VALUE_text.split('-')
+ if len(VALUE_text_list) == 3:
+ date_is_estimated = False
+
+ if VALUE_text_list[1].isalpha():
+ date_to_write = parse(VALUE_text).strftime('%Y-%m-%d')
+ elif len(VALUE_text_list) == 2:
+ date_to_write = VALUE_text + '-15'
+ else:
+ if int(VALUE_text) < 2020:
+ date_to_write = "{}-12-15".format(VALUE_text)
+ else:
+ date_to_write = "{}-01-15".format(VALUE_text)
+
+ info_for_yaml_dict['sample']['collection_date'] = date_to_write
+
+ if date_is_estimated:
+ 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(VALUE_text)
+ else:
+ info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(VALUE_text)
+ elif TAG_text == 'geo_loc_name':
+ if VALUE_text in term_to_uri_dict:
+ info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[VALUE_text]
+ elif VALUE_text.lower() not in ['na', 'not applicable']:
+ missing_value_list.append('\t'.join([accession, 'geo_loc_name', VALUE_text]))
+ #else:
+ # if TAG_text not in ['lat_lon', 'host_disease', 'BioSampleModel', 'passage_history']:
+ # print(accession, TAG_text, VALUE_text)
+
+
+ taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text
+ info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon_id
+
+
+ EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT')
+ INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0]
+ if INSTRUMENT_MODEL.lower() != 'unspecified':
+ if INSTRUMENT_MODEL in term_to_uri_dict:
+ info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]]
+ else:
+ missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL]))
+
+ LIBRARY_DESCRIPTOR = EXPERIMENT.find('DESIGN').find('LIBRARY_DESCRIPTOR')
+ if LIBRARY_DESCRIPTOR.text not in ['OTHER']:
+ info_for_yaml_dict['technology']['additional_technology_information'] = 'LIBRARY_STRATEGY: {};'.format(LIBRARY_DESCRIPTOR.find('LIBRARY_STRATEGY').text)
+
+
+ SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION')
+ info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession']
+
+ if SUBMISSION.attrib['lab_name'].lower() not in ['na']:
+ info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name']
+
+ STUDY = EXPERIMENT_PACKAGE.find('STUDY')
+ info_for_yaml_dict['submitter']['publication'] = SUBMISSION.attrib['lab_name']
+
+
+ Organization = EXPERIMENT_PACKAGE.find('Organization')
+ Organization_Name = Organization.find('Name')
+ info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text]
+
+ Organization_Contact = Organization.find('Contact')
+ if Organization_Contact is not None:
+ Organization_Contact_Name = Organization_Contact.find('Name')
+ info_for_yaml_dict['submitter']['submitter_name'] = [Organization_Contact_Name.find('First').text + ' ' + Organization_Contact_Name.find('Last').text]
+ info_for_yaml_dict['submitter']['additional_submitter_information'] = Organization_Contact.attrib['email']
+
+ Organization_Concact_Address = Organization_Contact.find('Address')
+ if Organization_Concact_Address is not None:
+ info_for_yaml_dict['submitter']['submitter_address'] = '; '.join([x.text for x in Organization_Concact_Address] + ['Postal code ' + Organization_Concact_Address.attrib['postal_code']])
+
+ Organization_Address = Organization.find('Address')
+ if Organization_Address is not None:
+ info_for_yaml_dict['submitter']['lab_address'] = '; '.join([x.text for x in Organization_Address] + ['Postal code ' + Organization_Address.attrib['postal_code']])
+
+ if 'collection_date' not in info_for_yaml_dict['sample']:
+ info_for_yaml_dict['sample']['collection_date'] = '1970-01-01'
+ info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing"
+
+ with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw:
+ json.dump(info_for_yaml_dict, fw, indent=2)
+
+if len(missing_value_list) > 0:
+ 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)) \ No newline at end of file
diff --git a/scripts/sequences.acc b/scripts/sequences.acc
deleted file mode 100644
index 697d868..0000000
--- a/scripts/sequences.acc
+++ /dev/null
@@ -1,1731 +0,0 @@
-NC_045512
-MT394528
-MT394529
-MT394530
-MT394531
-MT394864
-MT396241
-MT396242
-MT396243
-MT396244
-MT396245
-MT396246
-MT396247
-MT396248
-MT396266
-MT380726
-MT380727
-MT380728
-MT380729
-MT380730
-MT380731
-MT380732
-MT380733
-MT380734
-MT385414
-MT385415
-MT385416
-MT385417
-MT385418
-MT385419
-MT385420
-MT385421
-MT385422
-MT385423
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