aboutsummaryrefslogtreecommitdiff
path: root/scripts
diff options
context:
space:
mode:
authorPeter Amstutz2020-04-21 12:53:19 -0400
committerPeter Amstutz2020-04-21 12:53:19 -0400
commit88d81f853cf04b7f28681dd9cdee775b0422f252 (patch)
treeb23f5dedc100c8508784d20edaba864f91e7444d /scripts
parent85b85b676d7ecc218d9f84357b2e7ea0133eed94 (diff)
downloadbh20-seq-resource-88d81f853cf04b7f28681dd9cdee775b0422f252.tar.gz
bh20-seq-resource-88d81f853cf04b7f28681dd9cdee775b0422f252.tar.lz
bh20-seq-resource-88d81f853cf04b7f28681dd9cdee775b0422f252.zip
Working on NCBI import
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'scripts')
-rwxr-xr-xscripts/foreach.sh18
-rwxr-xr-x[-rw-r--r--]scripts/from_genbank_to_fasta_and_yaml.py26
2 files changed, 32 insertions, 12 deletions
diff --git a/scripts/foreach.sh b/scripts/foreach.sh
new file mode 100755
index 0000000..35b07b8
--- /dev/null
+++ b/scripts/foreach.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+rm -rf validated fasta_and_yaml_*
+mkdir -p validated
+./from_genbank_to_fasta_and_yaml.py
+fasta_files=$(find fasta_and_yaml_20200421/ -name "*.fasta")
+for f in $fasta_files ; do
+ yaml=$(echo $f | rev | cut -c7- | rev).yaml
+ echo $f
+ echo $yaml
+ if bh20-seq-uploader --validate $f $yaml ; then
+ sz=$(stat --format=%s $f)
+ if test $sz -gt 20000 ; then
+ mv $f $yaml validated
+ else
+ echo "Fasta file too small"
+ fi
+ fi
+done
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 7e7c089..1a12513 100644..100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,8 +1,10 @@
+#!/usr/bin/env python3
+
from Bio import Entrez
Entrez.email = 'another_email@gmail.com'
import xml.etree.ElementTree as ET
-import yaml
+import json
import os
from datetime import date
@@ -29,7 +31,7 @@ for term in term_list:
# Remove the version in the id
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
@@ -49,11 +51,11 @@ print(term_list + ['NCBI Virus'], len(id_set))
def chunks(lst, n):
for i in range(0, len(lst), n):
yield lst[i:i + n]
-
+
num_ids_for_request = 100
if not os.path.exists(dir_metadata_today):
os.makedirs(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_xxx_xml))
@@ -63,7 +65,7 @@ if not os.path.exists(dir_metadata_today):
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')]:
@@ -74,7 +76,7 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
if len(line.split(',')) > 2:
term, uri = line.strip('\n').split('",')
term = term.strip('"')
- else:
+ else:
term, uri = line.strip('\n').split(',')
term_to_uri_dict[term] = uri
@@ -125,7 +127,7 @@ if not os.path.exists(dir_fasta_and_yaml_today):
):
if info_to_check in GBSeq_comment_text:
tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-
+
if field_in_yaml == 'sequencing_coverage':
# A regular expression would be better!
info_for_yaml_dict['technology'][field_in_yaml] = ';'.join(
@@ -139,7 +141,7 @@ if not os.path.exists(dir_fasta_and_yaml_today):
seq_tec = term_to_uri_dict[seq_tec]
else:
print(accession_version, 'missing technologies:', seq_tec)
-
+
new_seq_tec_list.append(seq_tec)
for n, seq_tec in enumerate(new_seq_tec_list):
@@ -147,7 +149,7 @@ if not os.path.exists(dir_fasta_and_yaml_today):
else:
info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
-
+
#term_to_uri_dict
for GBFeature in GBSeq.iter('GBFeature'):
@@ -211,12 +213,12 @@ if not os.path.exists(dir_fasta_and_yaml_today):
info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
- #Remove technology key if empty!
+ # Remove technology key if empty!
if (info_for_yaml_dict['technology']=={}):
- del info_for_yaml_dict['key']
+ del info_for_yaml_dict['technology']
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()))
with open(os.path.join(dir_fasta_and_yaml_today, '{}.yaml'.format(accession_version)), 'w') as fw:
- yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)
+ json.dump(info_for_yaml_dict, fw, indent=2)