From 0e5a2352e4b3da6f28e8e0980680eb44111758cc Mon Sep 17 00:00:00 2001
From: Andrea Guarracino
Date: Sun, 31 May 2020 11:27:54 +0200
Subject: Updated the host_sex and host_age management
---
scripts/from_genbank_to_fasta_and_yaml.py | 62 ++++++++++++++++++++++++++-----
1 file changed, 52 insertions(+), 10 deletions(-)
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0c49c65..7c64b98 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -20,6 +20,13 @@ dir_dict_ontology_standardization = 'dict_ontology_standardization/'
today_date = date.today().strftime("%Y.%m.%d")
path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
+def is_integer(string_to_check):
+ try:
+ int(string_to_check)
+ return True
+ except ValueError:
+ return False
+
def chunks(lst, n):
for i in range(0, len(lst), n):
yield lst[i:i + n]
@@ -72,6 +79,7 @@ if not os.path.exists(dir_metadata):
Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
)
+
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')]:
@@ -109,6 +117,7 @@ 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 = {
@@ -195,21 +204,54 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
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]]
-
+ 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:
- if GBQualifier_value_text_list[1] in ['male', 'female']:
- if GBQualifier_value_text_list[1]=='male':
- info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384"
- elif GBQualifier_value_text_list[1]=='female':
- info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000383"
+ print(GBQualifier_value_text_list)
+ 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]]
+ 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, GBQualifier_name_text, GBQualifier_value_text_list[1]]))
+ 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 'age' in GBQualifier_value_text:
- info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[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]]))
+
+ print('host_sex {} - host_age {}'.format(host_sex, host_age), '<--', GBQualifier_value_text_list)
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
--
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