aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--scripts/from_genbank_to_fasta_and_yaml.py14
1 files changed, 9 insertions, 5 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index a7c9dc2..33615fa 100644
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,5 +1,5 @@
from Bio import Entrez
-Entrez.email = 'andresguarahino@gmail.com'
+Entrez.email = 'insert_your_email@gmail.com'
import xml.etree.ElementTree as ET
import yaml
@@ -54,7 +54,7 @@ if not os.path.exists(dir_metadata_today):
for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
path_metadata_xxx_xml = os.path.join(dir_metadata_today, 'metadata_{}.xml'.format(i))
- print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xml))
+ print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml))
with open(path_metadata_xxx_xml, 'w') as fw:
fw.write(
@@ -69,7 +69,11 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
with open(path_dict_xxx_csv) as f:
for line in f:
- term, uri = line.strip('\n').split(',')
+ 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
@@ -78,7 +82,7 @@ species_to_taxid_dict = {
}
-if os.path.exists(dir_fasta_and_yaml_today):
+if not os.path.exists(dir_fasta_and_yaml_today):
os.makedirs(dir_fasta_and_yaml_today)
for path_metadata_xxx_xml in [os.path.join(dir_metadata_today, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata_today) if name_metadata_xxx_xml.endswith('.xml')]:
@@ -203,7 +207,7 @@ if os.path.exists(dir_fasta_and_yaml_today):
info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
elif GBQualifier_name_text == 'db_xref':
info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1])
-
+
with open(os.path.join(dir_fasta_and_yaml_today, '{}.fasta'.format(accession_version)), 'w') as fw:
fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))