From 415e6022a4ad0d14a78f862441b69ca9edd95274 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 31 Mar 2021 18:44:17 +0200
Subject: [PATCH] use DSMZ match result with rewrite-taxonomy
---
rewrite-taxonomy.snakefile | 11 +++++++++++
1 file changed, 11 insertions(+)
create mode 100644 rewrite-taxonomy.snakefile
diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile
new file mode 100644
index 0000000..8ca2f6d
--- /dev/null
+++ b/rewrite-taxonomy.snakefile
@@ -0,0 +1,11 @@
+configfile: 'config.yaml'
+
+rule rewrite:
+ output:
+ config['OUTDIR'] + '/taxa+id_full_with-DSMZ.txt'
+
+ input:
+ config['OUTDIR'] + '/' + config['DSMZ_MATCH_DIR']
+
+ shell:
+ '''../bibliome-java-utils/test/install/bin/rewrite-taxonomy -namesFile {config[NCBI_NAMES_FILE]} -namesFile {input}/dsmz-names.dmp -prefix ncbi: -rejectionFile reject.txt -saturationFile saturate.txt -pattern '{{NAME}}\t{{TAXID}}\t{{CANONICAL}}\t{{TAXID_PATH}}\t{{POS_TAG}}\t{{RANK}}\t{{SPECIES_TAXID}}\t{{SPECIES_NAME}}\n' {config[NCBI_NODES_FILE]} {input}/dsmz-nodes.dmp >{output}'''
--
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