From a12fe94f174da766be612fbb2712b4db2ba98296 Mon Sep 17 00:00:00 2001
From: lltommy
Date: Wed, 22 Apr 2020 19:41:27 +0200
Subject: Small changes all around, trying to make the importer/metadata better

---
 scripts/foreach.sh                        |  2 +-
 scripts/from_genbank_to_fasta_and_yaml.py | 12 ++++++++----
 2 files changed, 9 insertions(+), 5 deletions(-)

(limited to 'scripts')

diff --git a/scripts/foreach.sh b/scripts/foreach.sh
index 35b07b8..ddc9387 100755
--- a/scripts/foreach.sh
+++ b/scripts/foreach.sh
@@ -2,7 +2,7 @@
 rm -rf validated fasta_and_yaml_*
 mkdir -p validated
 ./from_genbank_to_fasta_and_yaml.py
-fasta_files=$(find fasta_and_yaml_20200421/ -name "*.fasta")
+fasta_files=$(find fasta_and_yaml/ -name "*.fasta")
 for f in $fasta_files ; do
     yaml=$(echo $f | rev | cut -c7- | rev).yaml
     echo $f
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 00c0012..096a6af 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -8,10 +8,11 @@ import json
 import os
 
 from datetime import date
-today = date.today().strftime("%Y%m%d")
+#today = date.today().strftime("%Y%m%d")
 
-dir_metadata_today = 'metadata_from_nuccore_{}'.format(today)
-dir_fasta_and_yaml_today = 'fasta_and_yaml_{}'.format(today)
+
+dir_metadata_today = 'metadata_from_nuccore' #_{}'.format(today)
+dir_fasta_and_yaml_today = 'fasta_and_yaml' #'.format(today)
 
 dir_dict_ontology_standardization = 'dict_ontology_standardization/'
 
@@ -177,7 +178,10 @@ if not os.path.exists(dir_fasta_and_yaml_today):
 
                         if len(GBQualifier_value_text_list) > 1:
                             if GBQualifier_value_text_list[1] in ['male', 'female']:
-                                info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
+                                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"
                             else:
                                 info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1]
 
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