Mercurial > repos > bioitcore > splicetrap

comparison bin/get_event_dist_fit.pl @ 1:adc0f7765d85 draft

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planemo upload
author bioitcore
date Thu, 07 Sep 2017 15:06:58 -0400
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0:d4ca551ca300 1:adc0f7765d85
1 use Getopt::Long;
2 use strict;
3
4 use Cwd;
5 my $PROG = $0;
6 my $CUR_DIR = Cwd::abs_path(Cwd::cwd());
7 my $PROG_ABS_PATH = Cwd::abs_path($PROG);
8 my $SrcFolder=`dirname $PROG_ABS_PATH`;
9 chomp($SrcFolder);
10
11 #my $SrcFolder="/data/zhang/wuj/scripts/SpliceTrap.0.8/";
12 my $InputFileName=$ARGV[0];
13 my $OutputFileName = $ARGV[0].".hist";
14 #$OutputFileName=$ARGV[1] if $ARGV[1] ne "";
15 my $width=0.001;
16 my $verbose=1;
17 my $col=2;
18
19 GetOptions (
20 'w:f'=>\$width,
21 'c:i'=>\$col,
22 'v'=>\$verbose
23 );
24
25 $width=$width*1;
26 my $binnum=1/$width;
27 $col=$col-1;
28
29 my @CAratios;
30 my @CSratios;
31 my @ADratios;
32 my @AAratios;
33 my @AIratios;
34 my @IRratios;
35
36 open(Input, $InputFileName);
37 while(my $line=<Input>)
38 {
39 next if($line=~/^#/);
40 chomp($line);
41 my @array=split(/\s/,$line);
42 next if($array[$col]<=0.001 or $array[$col]>=0.999);
43 # push( @CAratios,$array[$col]) if($array[0]=~/^C[AS]/ or $array[0]=~/^ME/);
44 push( @CAratios,$array[$col]) if($array[0]=~/^CA/ or $array[0]=~/^ME/);
45 push( @CSratios,$array[$col]) if($array[0]=~/^CS/);
46 push( @ADratios,$array[$col]) if($array[0]=~/^AD/);
47 push( @AAratios,$array[$col]) if($array[0]=~/^AA/);
48 push( @AIratios,$array[$col]) if($array[0]=~/^AI/);
49 push( @IRratios,$array[$col]) if($array[0]=~/^IR/);
50
51 }
52
53 close(Input);
54
55 open(tmpFile, ">$InputFileName.tmpca");
56 for(my $i=0;$i<@CAratios;$i++)
57 {
58 print tmpFile $CAratios[$i],"\n";
59 }
60 close(tmpFile);
61 open(tmpFile, ">$InputFileName.tmpcs");
62 for(my $i=0;$i<@CSratios;$i++)
63 {
64 print tmpFile $CSratios[$i],"\n";
65 }
66 close(tmpFile);
67
68
69 open(tmpFile, ">$InputFileName.tmpad");
70 for(my $i=0;$i<@ADratios;$i++)
71 {
72 print tmpFile $ADratios[$i],"\n";
73 }
74 close(tmpFile);
75
76 open(tmpFile, ">$InputFileName.tmpaa");
77 for(my $i=0;$i<@AAratios;$i++)
78 {
79 print tmpFile $AAratios[$i],"\n";
80 }
81 close(tmpFile);
82
83 open(tmpFile, ">$InputFileName.tmpai");
84 for(my $i=0;$i<@AIratios;$i++)
85 {
86 print tmpFile $AIratios[$i],"\n";
87 }
88 close(tmpFile);
89
90 open(tmpFile, ">$InputFileName.tmpir");
91 for(my $i=0;$i<@IRratios;$i++)
92 {
93 print tmpFile $IRratios[$i],"\n";
94 }
95 close(tmpFile);
96
97 system("R --slave --args $InputFileName.tmpca <$SrcFolder/beta_fit.R");
98 system("R --slave --args $InputFileName.tmpad <$SrcFolder/beta_fit.R");
99 system("R --slave --args $InputFileName.tmpaa <$SrcFolder/beta_fit.R");
100 #system("R --slave --args $InputFileName.tmpai <$SrcFolder/R/beta_fit.R");
101 system("R --slave --args $InputFileName.tmpir <$SrcFolder/beta_fit.R");
102 system("R --slave --args $InputFileName.tmpcs <$SrcFolder/beta_fit.R");
103
104 system("echo '#Width:$width' >$InputFileName.fit.hist");
105 #system("paste $InputFileName.tmpca.fit $InputFileName.tmpad.fit $InputFileName.tmpaa.fit $InputFileName.tmpai.fit $InputFileName.tmpir.fit $InputFileName.tmpcs.fit >>$InputFileName.fit.hist");
106
107 system("paste $InputFileName.tmpca.fit $InputFileName.tmpad.fit $InputFileName.tmpaa.fit $InputFileName.tmpir.fit $InputFileName.tmpcs.fit >>$InputFileName.fit.hist");
108 #system("rm $InputFileName.tmpca* $InputFileName.tmpad* $InputFileName.tmpaa* $InputFileName.tmpai* $InputFileName.tmpir* ");