|
4
|
1 use strict;
|
|
|
2 use warnings;
|
|
|
3 use File::Basename;
|
|
|
4 use Cwd;
|
|
|
5 use File::Path qw(make_path remove_tree);
|
|
|
6 die qq(
|
|
|
7 Bad numbr of inputs
|
|
|
8
|
|
|
9 ) if(!@ARGV);
|
|
|
10
|
|
|
11 my @bam_list_entries;
|
|
|
12
|
|
|
13 my $player_options = "";
|
|
|
14 my $bam_file;
|
|
|
15 my $ending;
|
|
|
16 my $genome;
|
|
|
17 my $summary ;
|
|
|
18 my $output;
|
|
|
19
|
|
|
20 foreach my $input (@ARGV)
|
|
|
21 {
|
|
|
22 my @tmp = split "::", $input;
|
|
|
23 if($tmp[0] eq "GENOME")
|
|
|
24 {
|
|
|
25 $genome=$tmp[1];
|
|
|
26 }
|
|
|
27 elsif($tmp[0] eq "OPTION")
|
|
|
28 {
|
|
|
29 $player_options = "$player_options ${tmp[1]}";
|
|
|
30 }
|
|
|
31 elsif($tmp[0] eq "ENDING")
|
|
|
32 {
|
|
|
33 $ending = $tmp[1];
|
|
|
34 }
|
|
|
35 elsif($tmp[0] eq "BAMFILE")
|
|
|
36 {
|
|
|
37 $bam_file = $tmp[1];
|
|
|
38 }
|
|
|
39 elsif($tmp[0] eq "SUMMARY")
|
|
|
40 {
|
|
|
41 $summary = $tmp[1];
|
|
|
42 }
|
|
|
43 elsif($tmp[0] eq "OUTPUT")
|
|
|
44 {
|
|
|
45 $output = $tmp[1];
|
|
|
46 }
|
|
|
47 else
|
|
|
48 {
|
|
|
49 die("Unknown Input: $input\n");
|
|
|
50 }
|
|
|
51 }
|
|
|
52
|
|
|
53
|
|
|
54 my $working_dir = cwd();
|
|
|
55
|
|
|
56 #convert bam to sam
|
|
|
57 my $sam_file = "$working_dir/coverted.sam";
|
|
|
58 system("samtools view -h $bam_file > $sam_file");
|
|
|
59
|
|
|
60 #run bismark
|
|
|
61
|
|
|
62 system ("bismark_methylation_extractor $ending $player_options --genome_folder $genome $sam_file > $summary 2>&1");
|
|
|
63
|
|
|
64 move_files($working_dir);
|
|
|
65
|
|
|
66 sub move_files
|
|
|
67 {
|
|
|
68 my $name;
|
|
|
69 my $suffix;
|
|
|
70 my $path;
|
|
|
71 my $local_dir = $_[0];
|
|
|
72 opendir(DIR, $local_dir);
|
|
|
73 #print ("Openning: $local_dir\n");
|
|
|
74 my @FILES= readdir(DIR);
|
|
|
75 closedir(DIR);
|
|
|
76 foreach my $file (@FILES)
|
|
|
77 {
|
|
|
78 if ($file eq "." || $file eq "..")
|
|
|
79 {
|
|
|
80 #print ("./ or ../ skipped\n");
|
|
|
81 }
|
|
|
82 elsif (-d "$local_dir/$file")
|
|
|
83 {
|
|
|
84 #print ("moving to: $local_dir/$file\n");
|
|
|
85 move_files("$local_dir/$file");
|
|
|
86 }
|
|
|
87 elsif (-f "$local_dir/$file")
|
|
|
88 {
|
|
|
89 ($name,$path,$suffix) = fileparse($file,qr"\.[^.]*$");
|
|
|
90 if ($suffix eq ".bedGraph")
|
|
|
91 {
|
|
|
92 system ("mv $local_dir/$file $output");
|
|
|
93 }
|
|
|
94 }
|
|
|
95 else
|
|
|
96 {
|
|
|
97 die("Unrecognized file generated: $file\n");
|
|
|
98 }
|
|
|
99
|
|
|
100 }
|
|
|
101 }
|
|
|
102
|
|
|
103
|
|
|
104
|
|
|
105
|
|
|
106
|
