Skip to content
Snippets Groups Projects

Resolve "mise à jour des données de Genbank"

Merged Resolve "mise à jour des données de Genbank"
21-mise-a-jour-des-donnees-de-genbank into master
Merged Mouhamadou Ba requested to merge 21-mise-a-jour-des-donnees-de-genbank into master
Compare
and
Show latest version
1 file
+ 3
− 1
Compare changes
  • Side-by-side
  • Inline
process_GenBank_corpus.snakefile
+ 3
− 1
@@ -64,12 +64,14 @@ rule map_genbank_habitats:
@@ -64,12 +64,14 @@ rule map_genbank_habitats:
onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
graylist='ancillaries/graylist_extended.heads',
graylist='ancillaries/graylist_extended.heads',
emptywords='ancillaries/stopwords_EN.ttg'
emptywords='ancillaries/stopwords_EN.ttg',
 
inhibitSyntax='inhibit-syntax'
singularity:config["SINGULARITY_IMG"]
singularity:config["SINGULARITY_IMG"]
shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
-alias input {input.habitats} \
-alias input {input.habitats} \
-alias output {output.mapped_habitats}\
-alias output {output.mapped_habitats}\
-alias ontobiotope {params.onto} \
-alias ontobiotope {params.onto} \
 
-feat inhibit-syntax {params.inhibitSyntax} \
-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
{params.plan}
{params.plan}
"""
"""