Mercurial > repos > xuebing > splicesite_max_entropy

comparison splicesitescore/score3.pl @ 8:ec97befe722b

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author xuebing
date Sun, 01 Apr 2012 08:14:45 -0400
parents 85af77643e89
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7:3fd430270c0c 8:ec97befe722b
2 2
3 3
4 my $inputfile = $ARGV[0]; 4 my $inputfile = $ARGV[0];
5 my $usemaxent = 1; 5 my $usemaxent = 1;
6 6
7 7 my $modelpath = "/home/wuxbl/rowley/tools/maxentscan/splicemodels/";
8 my @metables = &makemaxentscores; 8 my @metables = &makemaxentscores($modelpath);
9 9
10 open (FILE,"<$inputfile") || die "can't open!\n"; 10 open (FILE,"<$inputfile") || die "can't open!\n";
11 11
12 while(<FILE>) { 12 while(<FILE>) {
13 chomp; 13 chomp;
49 } 49 }
50 return $sum; 50 return $sum;
51 } 51 }
52 52
53 sub makemaxentscores{ 53 sub makemaxentscores{
54 my $dir = "splicemodels/"; 54 my $dir = shift;
55 my @list = ('me2x3acc1','me2x3acc2','me2x3acc3','me2x3acc4', 55 my @list = ('me2x3acc1','me2x3acc2','me2x3acc3','me2x3acc4',
56 'me2x3acc5','me2x3acc6','me2x3acc7','me2x3acc8','me2x3acc9'); 56 'me2x3acc5','me2x3acc6','me2x3acc7','me2x3acc8','me2x3acc9');
57 my @metables; 57 my @metables;
58 my $num = 0 ; 58 my $num = 0 ;
59 foreach my $file (@list) { 59 foreach my $file (@list) {
69 #print STDERR $file."\t".$num."\t".$n."\n"; 69 #print STDERR $file."\t".$num."\t".$n."\n";
70 $num++; 70 $num++;
71 } 71 }
72 return @metables; 72 return @metables;
73 } 73 }
74 sub makewmmscores{ 74
75 my $dir = "splicemodels/";
76 my @list = ('me1s0acc1','me1s0acc2','me1s0acc3','me1s0acc4',
77 'me1s0acc5','me1s0acc6','me1s0acc7','me1s0acc8','me1s0acc9');
78 my @metables;
79 my $num = 0 ;
80 foreach my $file (@list) {
81 my $n = 0;
82 open (SCOREF,"<".$dir.$file) || die "Can't open $file!\n";
83 while(<SCOREF>) {
84 chomp;
85 $_=~ s/\s//;
86 $metables[$num]{$n} = $_;
87 $n++;
88 }
89 close(SCOREF);
90 #print STDERR $file."\t".$num."\t".$n."\n";
91 $num++;
92 }
93 return @metables;
94 }
95 sub makemmscores{
96 my $dir = "splicemodels/";
97 my @list = ('me2s0acc1','me2s0acc2','me2s0acc3','me2s0acc4',
98 'me2s0acc5','me2s0acc6','me2s0acc7','me2s0acc8','me2s0acc9');
99 my @metables;
100 my $num = 0 ;
101 foreach my $file (@list) {
102 my $n = 0;
103 open (SCOREF,"<".$dir.$file) || die "Can't open $file!\n";
104 while(<SCOREF>) {
105 chomp;
106 $_=~ s/\s//;
107 $metables[$num]{$n} = $_;
108 $n++;
109 }
110 close(SCOREF);
111 #print STDERR $file."\t".$num."\t".$n."\n";
112 $num++;
113 }
114 return @metables;
115 }
116 sub maxentscore{ 75 sub maxentscore{
117 my $seq = shift; 76 my $seq = shift;
118 my $table_ref = shift; 77 my $table_ref = shift;
119 my @metables = @$table_ref; 78 my @metables = @$table_ref;
120 my @sc; 79 my @sc;