~/bin/bam2hapInfo2PBS.pl
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#!/usr/bin/perl -w use strict; use Cwd; my $bam2hapinfo = "/home/shg047/bin/mergedBam2hapInfo.pl"; my $sample_info_file = $ARGV[0]; my $submit=$ARGV[1]; my %sample_group; die &USAGE if scalar(@ARGV)<1; open(INFILE, "$sample_info_file")||die("Error in opening file $sample_info_file.\n"); while(my $line = <INFILE>){ chop($line); my ($id,$bam_file, $target_bed) = split(/\t/, $line); next if(!$id || !$bam_file); $sample_group{$id}->{"bam_file"}=$bam_file; $sample_group{$id}->{"target_bed"}=$target_bed; } close(INFILE); foreach my $id (sort keys(%sample_group)){ next if $id=~/LambdaNEB/i; my $job_file_name = $id . ".job"; my $status_file = $id.".status"; my $hapInfo_file = $id.".hapInfo.txt"; my $curr_dir = `pwd`; open(JOB_FILE, ">$job_file_name") || die("Error in opening file $job_file_name.\n"); print JOB_FILE "#!/bin/csh\n"; print JOB_FILE "#PBS -q glean\n"; print JOB_FILE "#PBS -l nodes=1:ppn=1\n"; print JOB_FILE "#PBS -l walltime=8:00:00\n"; print JOB_FILE "#PBS -o ".$id.".log\n"; print JOB_FILE "#PBS -e ".$id.".err\n"; print JOB_FILE "#PBS -V\n"; print JOB_FILE "#PBS -M shihcheng.guo\@gmail.com \n"; print JOB_FILE "#PBS -m abe\n"; print JOB_FILE "#PBS -A k4zhang-group\n"; print JOB_FILE "cd $curr_dir\n"; my $cmd = "$bam2hapinfo ".$sample_group{$id}->{"target_bed"}." ".$sample_group{$id}->{"bam_file"}." > $hapInfo_file"; print JOB_FILE "$cmd\n"; close(JOB_FILE); print "Job file $job_file_name created.\n"; system("qsub $job_file_name"); } sub USAGE{ print "\nUSAGE: perl $0 sample_info_file submit\n\n"; print "Run to creat SamInfo if you don't have sample_info_file: \nperl ~/bin/samInfoPrep4Bam2Hapinfo.pl ./\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 ' }