From 3d2f458b6978426dff463c7ce7e39b41e3b31f12 Mon Sep 17 00:00:00 2001
From: derekwong90 <78445989+derekwong90@users.noreply.github.com>
Date: Fri, 30 Jun 2023 13:52:59 -0700
Subject: [PATCH] Create repeat_masker.sh

---
 repeat_masker/runner/repeat_masker.sh | 63 +++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100755 repeat_masker/runner/repeat_masker.sh

diff --git a/repeat_masker/runner/repeat_masker.sh b/repeat_masker/runner/repeat_masker.sh
new file mode 100755
index 0000000..714d3f9
--- /dev/null
+++ b/repeat_masker/runner/repeat_masker.sh
@@ -0,0 +1,63 @@
+INPUTDIR=/cluster/projects/pughlab/hereditary/external_data/TGL49_CHARM/LFS/LFS_WG/bams
+basedir=/cluster/projects/pughlab/hereditary/projects/CHARM/LFS/repeat_masker
+shdir=$basedir/sh_scripts
+outdir=$basedir/output
+sitedir=/cluster/projects/pughlab/hereditary/projects/CHARM/repeat_masker
+picard_dir=/cluster/tools/software/picard/2.10.9
+
+mkdir -p $shdir
+mkdir -p $outdir
+
+cd $sitedir
+ls *.bed > $shdir/sites
+
+cd $INPUTDIR
+ls *.bam > $shdir/bams
+
+cd $shdir
+sed 's/....$//' bams > bam
+mv bam bams
+sed 's/....$//' sites > site
+mv site sites
+
+for bam in $(cat bams); do
+
+name=$(echo $bam | sed 's/\_WG.*/_WG/')
+echo $bam
+echo $name
+
+mkdir -p $outdir/$name
+
+echo -e "#!/bin/bash\n
+module load picard\n" > $shdir/${name}.sh
+
+echo -e "java -jar $picard_dir/picard.jar CollectInsertSizeMetrics \
+I=$INPUTDIR/${bam}.bam \
+O=$outdir/$name/${name}_rm_genome.txt \
+H=$outdir/$name/${name}_rm_genome.pdf \
+M=0 \
+W=600" >> $shdir/${name}.sh
+
+for site in $(cat sites); do
+echo -e "### $site ###
+#samtools view -bh -L $sitedir/${site}.bed $INPUTDIR/${bam}.bam > $outdir/$name/${site}.bam
+#samtools index $outdir/$name/${site}.bam" >> $shdir/${name}.sh
+
+echo -e "#java -jar $picard_dir/picard.jar CollectInsertSizeMetrics \
+I=$outdir/$name/${site}.bam \
+O=$outdir/$name/${name}_rm_${site}.txt \
+H=$outdir/$name/${name}_rm_${site}.pdf \
+M=0 \
+W=600" >> $shdir/${name}.sh
+
+echo -e "#rm $outdir/$name/${site}.bam*\n" >> $shdir/${name}.sh
+
+done
+done
+
+cd $shdir
+
+ls *.sh > files
+for file in $(cat files); do
+sbatch -c 1 -t 24:00:00 -p all --mem 16G $file
+done