Reduce the footprint of the utr tool

cyversewarwick · Jan 24, 2017 · 459051b · 459051b
1 parent d5f0b8f
commit 459051b
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/bin/utr_tool/bo_utr.sh b/bin/utr_tool/bo_utr.sh
@@ -20,8 +20,8 @@ fi
 # 	mkdir outputs
 # fi
 
-cp $1 works/genome.fa
-cp $2 works/annot.gff3
+mv $1 works/genome.fa
+mv $2 works/annot.gff3
 
 cd works
 
@@ -34,6 +34,7 @@ grep -P '\tgene\t' annot.gff3 > genelines.gff3
 #strip the potential FASTA line breaks. creates genome_stripped.fa
 # cp $1 genome.fa
 python3 ../scripts/strip_newlines.py # genome.fa -> genome_stripped.fa
+rm genome.fa
 
 #create the .genome file
 samtools faidx genome_stripped.fa # creates .fai file

diff --git a/wrapper_de_utr.sh b/wrapper_de_utr.sh
@@ -24,10 +24,10 @@ cd /apples/bin/utr_tool
 
 ./bo_utr.sh $1 $2 $3 $4 $5 $6
 
-cp /apples/bin/utr_tool/works/promoters.fa /de-app-work/PlantA.fa
-cp /apples/bin/utr_tool/works/promoters.bed /de-app-work/PlantA.bed
-cp /apples/bin/utr_tool/works/utr3.bed /de-app-work/PlantA_utr3.bed
-cp /apples/bin/utr_tool/works/utr5.bed /de-app-work/PlantA_utr5.bed
+mv /apples/bin/utr_tool/works/promoters.fa /de-app-work/PlantA.fa
+mv /apples/bin/utr_tool/works/promoters.bed /de-app-work/PlantA.bed
+mv /apples/bin/utr_tool/works/utr3.bed /de-app-work/PlantA_utr3.bed
+mv /apples/bin/utr_tool/works/utr5.bed /de-app-work/PlantA_utr5.bed
 
 
 cd /de-app-work