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-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv357
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py30
-rw-r--r--scripts/sequences.acc297
3 files changed, 339 insertions, 345 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index c08b613..b81da36 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -1,328 +1,29 @@
-30.59 N 114.3 E,http://www.wikidata.org/entity/Q11746
-35.92 N 74.33 E,http://www.wikidata.org/entity/Q609024
-39.54 N 116.23 E,http://www.wikidata.org/entity/Q198244
-Afghanistan,http://www.wikidata.org/entity/Q889
-Albania,http://www.wikidata.org/entity/Q222
-Algeria,http://www.wikidata.org/entity/Q262
-Andorra,http://www.wikidata.org/entity/Q228
-Angola,http://www.wikidata.org/entity/Q916
-Antigua and Barbuda,http://www.wikidata.org/entity/Q781
-Argentina,http://www.wikidata.org/entity/Q414
-Armenia,http://www.wikidata.org/entity/Q399
-Australia,http://www.wikidata.org/entity/Q408
-Australia: Queensland,http://www.wikidata.org/entity/Q36074
-Australia: Victoria,http://www.wikidata.org/entity/Q36687
-Austria,http://www.wikidata.org/entity/Q40
-Azerbaijan,http://www.wikidata.org/entity/Q227
-Bahrain,http://www.wikidata.org/entity/Q398
-Bangladesh,http://www.wikidata.org/entity/Q902
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-China: Anhui,http://www.wikidata.org/entity/Q40956
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+aspirate,http://purl.obolibrary.org/obo/NCIT_C13347
+stool,http://purl.obolibrary.org/obo/NCIT_C13234
+serum,http://purl.obolibrary.org/obo/NCIT_C13325
+saliva,http://purl.obolibrary.org/obo/NCIT_C13275
+nasal swab,http://purl.obolibrary.org/obo/NCIT_C132119
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 148a7e1..21ed3b2 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -37,8 +37,7 @@ if not os.path.exists(dir_metadata):
tmp_list = [x.split('.')[0] for x in tmp_list]
print(term, len(tmp_list))
- tmp_list=tmp_list
- # tmp_list = tmp_list[0:2] # restricting to small run
+ #tmp_list = tmp_list[0:2] # restricting to small run
id_set.update([x.split('.')[0] for x in tmp_list])
@@ -112,13 +111,13 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
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
+ 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'] = ';'.join([x.text for x in GBSeq_references.iter('GBAuthor')])
+ 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:
@@ -126,7 +125,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
if GBReference_journal is not None and GBReference_journal.text != 'Unpublished':
if 'Submitted' in GBReference_journal.text:
- info_for_yaml_dict['submitter']['submitter_name'] = GBReference_journal.text.split(') ')[1].split(',')[0].strip()
+ info_for_yaml_dict['submitter']['submitter_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
@@ -146,8 +145,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
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>'))
+ 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
@@ -162,8 +162,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
new_seq_tec_list.append(seq_tec)
- for n, seq_tec in enumerate(new_seq_tec_list):
- info_for_yaml_dict['technology'][field_in_yaml + ('' if n == 0 else str(n + 1))] = seq_tec
+ 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
@@ -210,17 +209,14 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'
if GBQualifier_value_text in term_to_uri_dict:
- info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text]
+ info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[GBQualifier_value_text]]
else:
if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab', 'np/op']:
- info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab']
- info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab']
- elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab']:
- info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab']
- info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat 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']:
+ 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']
- info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['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':
diff --git a/scripts/sequences.acc b/scripts/sequences.acc
index a99c4e6..697d868 100644
--- a/scripts/sequences.acc
+++ b/scripts/sequences.acc
@@ -1,4 +1,299 @@
NC_045512
+MT394528
+MT394529
+MT394530
+MT394531
+MT394864
+MT396241
+MT396242
+MT396243
+MT396244
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+MT396266
+MT380726
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+MT380731
+MT380732
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+MT365033
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+MT374110
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+MT374112
+MT374113
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+MT375428
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+MT375451
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MT370516
MT370517
MT370518
@@ -225,6 +520,8 @@ MT372480
MT372481
MT372482
MT372483
+7BV2_P
+7BV2_T
LC542976
LC542809
MT114412