-
Notifications
You must be signed in to change notification settings - Fork 1
/
bam2hapinfoPBS.pl
67 lines (60 loc) · 4.37 KB
/
bam2hapinfoPBS.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
#!/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 "USAGE: perl $0 sample_info_file submit\n";
print "Run to creat SamInfo: perl 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
'
}