SamInfoPrep4Bam2Hapinfo.pl

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#!/usr/bin/perl
use strict;
use Cwd;
die &USAGE if scalar(@ARGV)<1;
my $bam_dir=shift @ARGV;
my $bed_dir="/home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed";
chdir $bam_dir;
my @file=glob("*.bam");
foreach my $file(@file){
my ($sample,undef)=split /\./,$file;
print "$sample\t$bam_dir$file\t$bed_dir\n";
}
sub USAGE{
print "USAGE: perl $0 bam_directory(TSCC)\n";
print '
Sample_Info_File Format:
ENCFF000LUN_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LUN_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LUP_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LUP_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LUQ_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LUQ_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LUT_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LUT_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LUU_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LUU_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LUV_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LUV_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LVA_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LVA_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LVB_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LVB_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LVE_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LVE_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LVF_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LVF_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LVI_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LVI_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
ENCFF000LVJ_trimmed /home/shg047/oasis/Haib/bam/ENCFF000LVJ_trimmed.fq.gz_bismark_bt2.sort.bam /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
'
}