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CGmapToolsMFG.pl
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CGmapToolsMFG.pl
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#!/usr/bin/perl
my @files = <J644*.CGmap.gz>;
for my $file (@files) {
open out, '>', "$file.sh";
print out "#!/bin/bash\n";
print out "#SBATCH --job-name=$file\n";
print out "#SBATCH --partition=batch\n";
print out "#SBATCH --ntasks=1\n";
print out "#SBATCH --nodes=1\n";
print out "#SBATCH --ntasks-per-node=1\n";
print out "#SBATCH --constraint=AMD\n";
print out "#SBATCH --time=18:00:00\n";
print out "#SBATCH --mem=10gb\n";
print out "module load CGmapTools/0.1.2-foss-2019b\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_synt_genes_up.bed -c 1 -x CG > $file.W22_synt_genes.CG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_synt_genes_up.bed -c 1 -x CHG > $file.W22_synt_genes.CHG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_synt_genes_up.bed -c 1 -x CHH > $file.W22_synt_genes.CHH.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_synt_genes_down.bed -c 1 -x CG > $file.W22_synt_genes.CG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_synt_genes_down.bed -c 1 -x CHG > $file.W22_synt_genes.CHG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_synt_genes_down.bed -c 1 -x CHH > $file.W22_synt_genes.CHH.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_Gypsy_intact_up.bed -c 1 -x CG > $file.W22_Gypsy_intact.CG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_Gypsy_intact_up.bed -c 1 -x CHG > $file.W22_Gypsy_intact.CHG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_Gypsy_intact_up.bed -c 1 -x CHH > $file.W22_Gypsy_intact.CHH.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_Gypsy_intact_down.bed -c 1 -x CG > $file.W22_Gypsy_intact.CG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_Gypsy_intact_down.bed -c 1 -x CHG > $file.W22_Gypsy_intact.CHG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r ~/references/W22_Gypsy_intact_down.bed -c 1 -x CHH > $file.W22_Gypsy_intact.CHH.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_hyperDMRs_UP_sort.bed -c 1 -x CG > $file.wt_endo-embryo_hyperDMR.CG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_hyperDMRs_UP_sort.bed -c 1 -x CHG > $file.wt_endo-embryo_hyperDMR.CHG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_hyperDMRs_UP_sort.bed -c 1 -x CHH > $file.wt_endo-embryo_hyperDMR.CHH.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_hyperDMRs_DOWN_sort.bed -c 1 -x CG > $file.wt_endo-embryo_hyperDMR.CG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_hyperDMRs_DOWN_sort.bed -c 1 -x CHG > $file.wt_endo-embryo_hyperDMR.CHG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_hyperDMRs_DOWN_sort.bed -c 1 -x CHH > $file.wt_endo-embryo_hyperDMR.CHH.down.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_hyperDMRs_UP_sort.bed -c 1 -x CG > $file.wt-mdr1_endo_hyperDMR.CG.up.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_hyperDMRs_UP_sort.bed -c 1 -x CHG > $file.wt-mdr1_endo_hyperDMR.CHG.up.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_hyperDMRs_UP_sort.bed -c 1 -x CHH > $file.wt-mdr1_endo_hyperDMR.CHH.up.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_hyperDMRs_DOWN_sort.bed -c 1 -x CG > $file.wt-mdr1_endo_hyperDMR.CG.down.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_hyperDMRs_DOWN_sort.bed -c 1 -x CHG > $file.wt-mdr1_endo_hyperDMR.CHG.down.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_hyperDMRs_DOWN_sort.bed -c 1 -x CHH > $file.wt-mdr1_endo_hyperDMR.CHH.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_EMRs_UP_sort.bed -c 1 -x CG > $file.wt_endo-embryo_EMR.CG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_EMRs_UP_sort.bed -c 1 -x CHG > $file.wt_endo-embryo_EMR.CHG.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_EMRs_UP_sort.bed -c 1 -x CHH > $file.wt_endo-embryo_EMR.CHH.up.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_EMRs_DOWN_sort.bed -c 1 -x CG > $file.wt_endo-embryo_EMR.CG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_EMRs_DOWN_sort.bed -c 1 -x CHG > $file.wt_endo-embryo_EMR.CHG.down.mfg\n";
#print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt_endo-embryo_EMRs_DOWN_sort.bed -c 1 -x CHH > $file.wt_endo-embryo_EMR.CHH.down.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_EMRs_UP_sort.bed -c 1 -x CG > $file.wt-mdr1_endo_EMR.CG.up.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_EMRs_UP_sort.bed -c 1 -x CHG > $file.wt-mdr1_endo_EMR.CHG.up.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_EMRs_UP_sort.bed -c 1 -x CHH > $file.wt-mdr1_endo_EMR.CHH.up.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_EMRs_DOWN_sort.bed -c 1 -x CG > $file.wt-mdr1_endo_EMR.CG.down.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_EMRs_DOWN_sort.bed -c 1 -x CHG > $file.wt-mdr1_endo_EMR.CHG.down.mfg\n";
print out "gunzip -c $file | cgmaptools mfg -r /scratch/gent/regions/wt-mdr1_endo_EMRs_DOWN_sort.bed -c 1 -x CHH > $file.wt-mdr1_endo_EMR.CHH.down.mfg\n";
print "sbatch $file.sh\n";
system "sbatch $file.sh";
}