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 ' }