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authorPjotr Prins2021-01-01 12:27:00 +0000
committerPjotr Prins2021-01-01 12:27:00 +0000
commita86633121cd92e37b2353f4bba8f2c37fa970d05 (patch)
tree5bd64dc5c71633fc842dc3092f7fabef24750ca4 /workflows/pull-data/genbank
parent2c6181c7eb86c0285928a434a37401d6680f9f79 (diff)
downloadbh20-seq-resource-a86633121cd92e37b2353f4bba8f2c37fa970d05.tar.gz
bh20-seq-resource-a86633121cd92e37b2353f4bba8f2c37fa970d05.tar.lz
bh20-seq-resource-a86633121cd92e37b2353f4bba8f2c37fa970d05.zip
genbank-fetch-ids.py
Diffstat (limited to 'workflows/pull-data/genbank')
-rw-r--r--workflows/pull-data/genbank/README.md2
-rw-r--r--workflows/pull-data/genbank/utils.py62
2 files changed, 63 insertions, 1 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
index f442b5d..d7c294b 100644
--- a/workflows/pull-data/genbank/README.md
+++ b/workflows/pull-data/genbank/README.md
@@ -4,7 +4,7 @@
# --- get list of IDs already in PubSeq
sparql-fetch-ids > pubseq_ids.txt
# --- get list of missing genbank IDs
-genbank-fetch-ids --skip pubseq_ids.txt > genbank_ids.txt
+genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
# --- fetch XML
update-from-genbank.py --ids genbank_ids.txt --outdir ~/tmp/genbank
# --- Transform to YAML and FASTA
diff --git a/workflows/pull-data/genbank/utils.py b/workflows/pull-data/genbank/utils.py
new file mode 100644
index 0000000..3efc67a
--- /dev/null
+++ b/workflows/pull-data/genbank/utils.py
@@ -0,0 +1,62 @@
+import os
+
+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]
+
+def check_and_get_ontology_dictionaries(dir_ontology_dictionaries):
+ # Check duplicated entry looking at all dictionaries
+ field_to_term_to_uri_dict = {}
+
+ path_dict_xxx_csv_list = [os.path.join(dir_ontology_dictionaries, name_xxx_csv) for name_xxx_csv in
+ os.listdir(dir_ontology_dictionaries) if name_xxx_csv.endswith('.csv')]
+
+ for path_dict_xxx_csv in path_dict_xxx_csv_list:
+ print('Read {}'.format(path_dict_xxx_csv))
+
+ with open(path_dict_xxx_csv) as f:
+ for line in f:
+ if len(line.split(',')) > 2:
+ term, uri = line.strip('\n').split('",')
+ else:
+ term, uri = line.strip('\n').split(',')
+
+ term = term.strip('"')
+
+ if term in field_to_term_to_uri_dict:
+ print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
+ continue
+
+ field_to_term_to_uri_dict[term] = uri
+
+ # Prepare separated dictionaries (to avoid, for example, that a valid IRI for species is accepted as specimen)
+ field_to_term_to_uri_dict = {}
+
+ for path_dict_xxx_csv in path_dict_xxx_csv_list:
+ field = os.path.basename(path_dict_xxx_csv).split('.')[0]
+
+ field_to_term_to_uri_dict[field] = {}
+
+ with open(path_dict_xxx_csv) as f:
+ for line in f:
+ if len(line.split(',')) > 2:
+ term, uri = line.strip('\n').split('",')
+ else:
+ term, uri = line.strip('\n').split(',')
+
+ term = term.strip('"')
+
+ if term in field_to_term_to_uri_dict[field]:
+ print('Warning: in the {} dictionary there are more entries for the same term ({}).'.format(field, term))
+ continue
+
+ field_to_term_to_uri_dict[field][term] = uri
+
+ return field_to_term_to_uri_dict \ No newline at end of file