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absrel.sh
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#!/bin/bash -l
#SBATCH -D /home/dmvelasc/Projects/Prunus/Analysis/selection
#SBATCH -o /home/dmvelasc/Projects/Prunus/slurm-log/%A_%a-absrel-stdout.txt
#SBATCH -e /home/dmvelasc/Projects/Prunus/slurm-log/%A_%a-absrel-stderr.txt
#SBATCH -J absrel
#SBATCH -a 1986-4736%15
#SBATCH -t 8-00:00:00
#SBATCH -p bigmemm
#SBATCH -n 1
#SBATCH -c 2
#SBATCH --exclude=bigmem1,bigmem2,bigmem3
#SBATCH --mail-user=dmvelasco@ucdavis.edu
#SBATCH --mail-type=ALL
set -e
set -u
# number of genes with evidence of selection from BUSTED = number of arrays = 4736
### Load modules ###
module load hyphy
# Declare number variables
x=$SLURM_ARRAY_TASK_ID
i=$(( x-1 ))
### Declare directories ###
ref="/home/dmvelasc/Data/references/persica-SCF" # reference directory
gene_list="/home/dmvelasc/Projects/Prunus/Analysis/selection/busted_p-values.txt" # gene list
FASTAdir="/home/dmvelasc/Projects/Prunus/Data/fasta/fasta-nostop" # final fasta directory
script="/home/dmvelasc/Projects/Prunus/Script" # script directory that includes batch file and consensus tree
batchdir="/share/apps/hyphy-2.3.14/lib/hyphy/TemplateBatchFiles/SelectionAnalyses" # BUSTED batch file directory
finaldir="/home/dmvelasc/Projects/Prunus/Analysis/select_branches"
#### sample ID file
# column 1: ID, column2: other ID/information
#list="/home/dmvelasc/Projects/Prunus/Script/sample.txt"
echo -e "extract sample ID from ${gene_list} using mapfile"
date
mapfile -s "$i" -n 1 -t id < "${gene_list}"
# declare gene ID variable from array
gene=( `echo "${id[0]}"` )
gene_id="${gene[0]}"
echo -e "Starting aBSREL analysis for ${gene_id}"
date
##### a B s R e L #####
if [ -s "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta" ]
# if file exists and is not empty
then
#HYPHYMP LIBPATH=/share/apps/hyphy-2.3.14/lib/ "${batchdir}"/aBSREL.bf "Universal" "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta" "${script}/splitstree_all.tree" "All" "" > "$finaldir"/"${gene_id}_cds_absrel.txt"
# HYPHYMP LIBPATH=/share/apps/hyphy-2.3.14/lib/ "${batchdir}"/aBSREL.bf "Universal" "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta" "${script}/split_alltest2_final_4_rooted_busted.nwk" "All" "" "${finaldir}/${gene_id}_cds_absrel.out" > "${finaldir}/${gene_id}_cds_absrel.txt"
HYPHYMP LIBPATH=/share/apps/hyphy-2.3.14/lib/hyphy "${batchdir}"/aBSREL.bf "Universal" "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta" "${script}/split_alltest2_final_4_rooted.nwk" "All" "" "${finaldir}/${gene_id}_cds_absrel.out" > "${finaldir}/${gene_id}_cds_absrel.txt"
# if [ -s "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta.BUSTED.json" ]
# then
# mv "${FASTAdir}/${gene_id}_cds_aln_nostop.fasta.BUSTED.json" "$finaldir"
# fi
#HYPHYMP LIBPATH=/share/apps/hyphy-2.3.14/lib/ "${batchdir}"/aBSREL.bf "Universal" "${FASTAdir}/${gene_id}_cds.aln" "${script}/split_alltest2_final_4_rooted.nwk" "All" "" > "$finaldir"/"${gene_id}_cds_absrel_none.txt"
# what is output directory? same as input directory. what is output file? BUSTED.json
fi
echo -e "aBSREL analysis finished"
date