From 099dbcbd1c5313f75076d7d65a122dc2d4c69280 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Mon, 5 Apr 2021 14:29:46 +0200
Subject: [PATCH] simpler snakefiles
---
config.yaml | 3 +--
dsmz-match.snakefile | 2 +-
rewrite-taxonomy.snakefile | 2 +-
3 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/config.yaml b/config.yaml
index 42faed3..151fab9 100644
--- a/config.yaml
+++ b/config.yaml
@@ -8,8 +8,7 @@ ALVISNLP: '~/code/alvisnlp/.test/alvisnlp/bin/alvisnlp'
# NCBI Taxonomy files
-NCBI_NODES_FILE: 'ncbi-taxonomy/nodes.dmp'
-NCBI_NAMES_FILE: 'ncbi-taxonomy/names.dmp'
+NCBI_DIR: 'ncbi-taxonomy_2021-03-26'
# Output and working directories
diff --git a/dsmz-match.snakefile b/dsmz-match.snakefile
index 832e9bb..30dd51e 100644
--- a/dsmz-match.snakefile
+++ b/dsmz-match.snakefile
@@ -14,4 +14,4 @@ rule match:
match='./dsmz-match.py',
strains=config['OUTDIR'] + '/' + config['DSMZ_STRAINS_DIR']
- shell: '''{input.match} {config[NCBI_NODES_FILE]} {config[NCBI_NAMES_FILE]} {input.strains} {output}'''
+ shell: '''{input.match} {config[NCBI_DIR]}/nodes.dmp {config[NCBI_DIR]}/names.dmp {input.strains} {output}'''
diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile
index 8ca2f6d..2fbefe5 100644
--- a/rewrite-taxonomy.snakefile
+++ b/rewrite-taxonomy.snakefile
@@ -8,4 +8,4 @@ rule rewrite:
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}'''
+ '''../bibliome-java-utils/test/install/bin/rewrite-taxonomy -namesFile {config[NCBI_DIR]}/names.dmp -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_DIR]}/nodes.dmp {input}/dsmz-nodes.dmp >{output}'''
--
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