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comparison filterReadsByLength.pl @ 1:f97b6074c41b draft default tip

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author big-tiandm
date Wed, 02 Jul 2014 02:41:30 -0400
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0:217f9663d891 1:f97b6074c41b
1 #!/usr/bin/perl -w
2 #Filename:
3 #Author: Tian Dongmei
4 #Email: tiandm@big.ac.cn
5 #Date: 2010-01
6 #Modified:
7 #Description:
8 my $version=1.00;
9
10 use strict;
11 use Getopt::Long;
12 use File::Basename;
13
14 my %opts;
15 GetOptions(\%opts,"i=s","min=i","max=i","o=s","mark:s","h");
16 if (!(defined $opts{i} and defined $opts{o} and defined $opts{min} and defined $opts{max}) || defined $opts{h}) { #necessary arguments
17 &usage;
18 }
19
20 my $mark=defined $opts{'mark'} ? $opts{'mark'} : "Sample";
21 my @mark=split /,/,$mark;
22
23
24 open OUT,">$opts{o}";
25 open IN,"<$opts{i}";
26 my %hash;my %reads;
27 while (my $aline=<IN>) {
28 chomp $aline;
29 my $seq=<IN>;
30 chomp $seq;
31
32 if($aline=~/:([\d|_]+)_x(\d+)$/){
33 my @ss=split/_/,$1;
34 for (my $i=0;$i<@ss;$i++) {
35 $hash{length($seq)}[$i]++ if($ss[$i]>0);
36 $hash{length($seq)}[$i] +=0 if($ss[$i]>0);
37 $reads{length($seq)}[$i]+=$ss[$i];
38 }
39 }
40 #else{$reads{length($seq)}+=1;}
41 if (length ($seq)>=$opts{'min'} && length ($seq) <=$opts{'max'}) {
42 print OUT "$aline\n$seq\n";
43 }
44 }
45 close IN;
46 close OUT;
47
48 my $dir=dirname($opts{'o'});
49 chdir $dir;
50 my $lengthfile=$dir."/reads_length_distribution.txt";
51 open OUT, ">$lengthfile";
52 open R,">$dir/length_distribution.R";
53
54 print OUT "Tags length\t@mark\n";
55
56 my $samNo=@mark;
57 my $avalue="";
58 my @length=sort{$a<=>$b} keys %hash;
59 foreach (@length) {
60 print OUT $_,"\t@{$hash{$_}}\n";
61 my $vv=join ", ",@{$hash{$_}};
62 $avalue .="$vv,";
63 }
64 $avalue =~s/,$//;
65 my $lengths=join ",",@length;
66 my $marks=join "\",\"",@mark;
67
68 print R "a<-c($avalue)
69 b<-matrix(a,ncol=$samNo,byrow=T)
70 cl<-colors()
71 names=c($lengths)
72 legends=c(\"$marks\")
73 png(\"Tags_length.png\",width=800,height=600)
74 barplot(t(b),beside=TRUE,col=cl[1:$samNo],main=\"Tags Length Distribution\",names.arg=names,ylim=c(0,max(a)),legend.text=legends,args.legend=\"topleft\")
75 abline(h=0)
76 dev.off()
77
78 ";
79 $avalue="";
80 print OUT "\nReads length\t@mark\n";
81 foreach (@length) {
82 print OUT $_,"\t@{$reads{$_}}\n";
83 my $vv=join ", ", @{$reads{$_}};
84 $avalue .= "$vv,";
85 }
86 $avalue =~s/,$//;
87
88 print R "a<-c($avalue)\n
89 b<-matrix(a,ncol=$samNo,byrow=T)
90
91 png(\"Reads_length.png\",width=800,height=600)
92 barplot(t(b),beside=TRUE,col=cl[1:$samNo],main=\"Reads Length Distribution\",names.arg=names,ylim=c(0,max(a)),legend.text=legends,args.legend=\"topleft\")
93 abline(h=0)
94 dev.off()
95
96 ";
97 close OUT;
98 close R;
99
100 system ("R CMD BATCH $dir/length_distribution.R");
101
102 #system ("rm $dir/length_distribution.R");
103 #system ("rm $dir/length_distribution.Rout");
104 #system ("rm $dir/.RData");
105 sub usage{
106 print <<"USAGE";
107 Version $version
108 Usage:
109 $0 -i -o -min -max -mark
110 options:
111
112 -i input file
113 -o output file
114 -min reads min length.
115 -max reads max length.
116 -mark string #sample name eg: samA,samB,samC
117 -h help
118 USAGE
119 exit(1);
120 }
121