annotate scripts/pickSoftClipping.over.pl @ 10:3200a0299230 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
author portiahollyoak
date Wed, 27 Apr 2016 11:44:13 -0400
parents 28d1a6f8143f
children 9672fe07a232
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
1 #!/share/bin/perl
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
2 use Bio::Seq;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
3 use List::Util qw(sum);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
4
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
5 die "perl $0 <*.excision.cluster.rpmk> <Reference.2bit>\n" if @ARGV<1;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
6
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
7 my $title=$ARGV[0];
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
8 if ($title =~ /annotation/) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
9 $title =~ s/excision.cluster.annotation/sorted.bam/;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
10 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
11 else {$title =~ s/excision.cluster.rpmk/sorted.bam/;}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
12
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
13 my %chrs=();
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
14 system("samtools view -H $title > header");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
15 open (input, "<header") or die "Can't open header since $!\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
16 while (my $line=<input>) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
17 if ($line =~ /^\@SQ/) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
18 my @a=split(/\t/, $line);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
19 for my $j (0..$#a) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
20 if ($a[$j] =~ /^SN:/) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
21 $a[$j] =~ s/^SN://;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
22 $chrs{$a[$j]}=1;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
23 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
24 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
25 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
26 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
27 close input;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
28 system("rm header");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
29
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
30 open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
31 while (my $line=<input>) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
32 chomp($line);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
33 my @a=split(/\s+/, $line);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
34
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
35 my $lower=$a[3]-100;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
36 my $upper=$a[4]+100;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
37 my $chr_num=$a[2];
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
38 $chr_num =~ s/chr//;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
39 if (($chrs{$a[2]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[2];}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
40 system("samtools view -bu $title $chr_num\:$lower\-$upper > temp.bam");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
41 system("samtools view -Xf 0x2 temp.bam > temp.sam");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
42
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
43 my $leftseq="";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
44 my $rightseq="";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
45
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
46 my $ll=$a[3]-150;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
47 my $lu=$a[3]+150;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
48 system("twoBitToFa $ARGV[1] -seq=$a[2] -start=$ll -end=$lu left.fa");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
49 open (seq, "<left.fa") or die "Can't open left.fa since $!\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
50 my $head=<seq>;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
51 for my $k (0..5) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
52 $head=<seq>;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
53 chomp($head);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
54 $leftseq=$leftseq."$head";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
55 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
56 $leftseq=uc($leftseq);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
57 close seq;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
58 system("rm left.fa");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
59
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
60 my $rl=$a[4]-150;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
61 my $ru=$a[4]+150;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
62 system("twoBitToFa $ARGV[1] -seq=$a[2] -start=$rl -end=$ru right.fa");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
63 open (seq, "<right.fa") or die "Can't open right.fa since $!\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
64 my $head=<seq>;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
65 for my $k (0..5) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
66 $head=<seq>;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
67 chomp($head);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
68 $rightseq=$rightseq."$head";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
69 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
70 $rightseq=uc($rightseq);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
71 close seq;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
72 system("rm right.fa");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
73
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
74
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
75 open in,"temp.sam";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
76 my %pe=();
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
77 while(<in>)
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
78 {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
79 chomp;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
80 my @f=split/\t/,$_,12;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
81 ## read number 1 or 2
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
82 my ($rnum)=$f[1]=~/(\d)$/;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
83
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
84 ## XT:A:*
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
85 my ($xt)=$f[11]=~/XT:A:(.)/;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
86
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
87 my $CIGAR=$f[5];
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
88 $CIGAR =~ s/S//g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
89 if ($f[5]=~/S/) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
90
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
91 ## Coordinate
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
92 my $coor=-10;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
93 my $overcoor=-10;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
94 my $strand="";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
95 my @z=split(/M/, $f[5]);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
96
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
97 if (($f[5]=~/S$/)&&($f[1]=~/r/))
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
98 {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
99 my (@cigar_m)=$f[5]=~/(\d+)M/g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
100 my (@cigar_d)=$f[5]=~/(\d+)D/g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
101 my (@cigar_s)=$f[5]=~/(\d+)S/g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
102 my (@cigar_i)=$f[5]=~/(\d+)I/g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
103 my $aln_ln=sum(@cigar_m,@cigar_d);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
104 $coor=$f[3]+$aln_ln-1;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
105 $strand="-";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
106
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
107 my (@clipped)=$z[1]=~/(\d+)S/g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
108 my $cliplen=sum(@clipped);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
109 # print "$f[0]\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
110 # print "$cliplen\t";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
111 if ($cliplen >= 10) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
112 my $clipseq=substr($f[9], length($f[9])-$cliplen, $cliplen);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
113 $overcoor = index($rightseq, $clipseq);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
114 # print "$clipseq\t$rightseq\t$overcoor\t";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
115 if ($overcoor > -1) {$overcoor += ($a[4] - 149);}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
116 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
117 # print "\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
118 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
119 elsif (($f[1]=~/R/)&&($z[0]=~/S/)) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
120 $coor=$f[3]; $strand="+";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
121 my (@clipped)=$z[0]=~/(\d+)S/g;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
122 my $cliplen=sum(@clipped);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
123 # print "$f[0]\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
124 # print "$cliplen\t";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
125 if ($cliplen >= 10) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
126 my $clipseq=substr($f[9], 0, $cliplen);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
127 $overcoor = index($leftseq, $clipseq);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
128 # print "$clipseq\t$leftseq\t$overcoor\t";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
129 if ($overcoor > -1) {$overcoor += ($a[3] - 150 + $cliplen);}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
130 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
131 # print "\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
132 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
133
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
134 if ($coor > 0) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
135 my $final="";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
136 if ($overcoor > 0) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
137 if ($strand eq "-") {$final="$coor\-$overcoor"."\($strand\)";}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
138 else {$final="$overcoor\-$coor"."\($strand\)";}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
139 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
140 else {$final=$coor."\($strand\)";}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
141 if (defined $pe{$final}) {$pe{$final}++;}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
142 else {$pe{$final}=1;}
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
143 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
144
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
145 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
146 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
147 close in;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
148
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
149 my $clip_site="";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
150
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
151 foreach my $coor (keys %pe)
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
152 {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
153 if ($pe{$coor} >= 2) {
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
154 $clip_site=$clip_site."$coor\:$pe{$coor}\;";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
155 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
156 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
157
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
158 chop($clip_site);
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
159 print "$a[2]\t$a[3]\t$a[4]\t$a[5]\t$clip_site\n";
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
160 system("rm temp.sam temp.bam");
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
161 # last;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
162 }
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
parents:
diff changeset
163