Mercurial > repos > matces > carpet_toolsuite

annotate carpet-src-1/tools/CARPET/MapToExon_RefSeqMat_new.pl @ 1:78770028dcf1 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:59:33 -0400
parents cdd489d98766
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
1 #!/usr/bin/perl
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
2
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
3 # Copyright 2009 Matteo Cesaroni, Lucilla Luzi
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
4 #
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
5 # This program is free software; ; you can redistribute it and/or modify
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
6 # it under the terms of the GNU Lesser General Public License as published by
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
7 # the Free Software Foundation; either version 3 of the License, or (at your
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
8 # option) any later version.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
9 #
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
10 # This program is distributed in the hope that it will be useful,
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
13 # GNU General Public License for more details.
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
14
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
15
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
16 $|=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
17 my $infile = $ARGV[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
18 my $infile2=$ARGV[1];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
19 my $definition_pro=$ARGV[2];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
20 my $definition_tre=$ARGV[3];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
21 my $priority=$ARGV[4];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
22 my $file_output=$ARGV[5];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
23
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
24 open (INFILE, "<$infile");
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
25 open (INFILE2, "<$infile2");
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
26 open (OUTFILE1, ">$file_output") or die "Cannot find file $file_output\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
27
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
28 $campi_t=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
29 $definition_out=$definition_pro-2000;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
30
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
31 while (defined (my $line_down = <INFILE2>)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
32 $line_down=~ s/\#//g;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
33 chomp($line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
34 $campi_t++;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
35 my @tmp_down=split(/\s+/, $line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
36 if($campi_t==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
37 $z=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
38 foreach $campo_t(@tmp_down){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
39 if(($campo_t eq "name") || ($campo_t eq "qName") || ($campo_t eq "repClass")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
40 $zRef=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
41 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
42 if(($campo_t eq "txStart") || ($campo_t eq "tStart") || ($campo_t eq "chromStart")|| ($campo_t eq "genoStart")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
43 $ztxStart=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
44 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
45 if(($campo_t eq "txEnd") || ($campo_t eq "tEnd") || ($campo_t eq "chromEnd")|| ($campo_t eq "genoEnd")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
46 $ztxEnd=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
47 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
48 if($campo_t eq "strand"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
49 $zstrand=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
50 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
51 if(($campo_t eq "chrom") || ($campo_t eq "tName")|| ($campo_t eq "genoName")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
52 $zchrom=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
53 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
54 if(($campo_t eq "exonStarts") || ($campo_t eq "tStarts")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
55 $zexonstart=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
56 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
57 if($campo_t eq "exonEnds"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
58 $zexonend=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
59 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
60 if($campo_t eq "blockSizes"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
61 $zblocksize=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
62 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
63 if(($campo_t eq "name2") || ($campo_t eq "repFamily")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
64 $zname=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
65 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
66 if(($campo_t eq "exonCount")||($campo_t eq "blockCount")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
67 $zcount=$z;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
68 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
69 $z++;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
70 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
71 if(!$zname){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
72 $zname=$zRef;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
73 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
74 if(!$zexonstart){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
75 $zexonstart=$ztxStart;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
76 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
77 if(!$zexonend){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
78 $zexonend=$ztxEnd;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
79 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
80 if(($zRef eq "") || ($ztxStart eq "") || ($zstrand eq "") || ($zchrom eq "")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
81 print "Annotation file is not in the accepted format\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
82 exit;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
83 }else{print "promoter=$definition_pro, priority=$priority";}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
84 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
85 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
86 chomp $tmp_down[$zchrom];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
87 $tab_ann{$tmp_down[$zchrom]}.="$line_down\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
88 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
89
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
90 while (defined (my $line_down = <INFILE>)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
91 my @tmp_down = split("\t", $line_down);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
92 chomp $tmp_down[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
93 $tab_probe{$tmp_down[0]}.=$line_down;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
94 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
95
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
96 @chrom_probes= keys(%tab_probe);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
97
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
98 &chip;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
99
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
100 exit 0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
101
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
102 ###########
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
103 #subrutine#
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
104 ###########
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
105
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
106 sub chip
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
107 {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
108 foreach $chromosoma (@chrom_probes){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
109
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
110 @file1=split("\n", $tab_probe{$chromosoma});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
111
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
112 foreach $line(@file1) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
113 chomp $line;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
114 #chop $line;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
115 if ($line=~/track/g){next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
116 if ($line=~/#/g){next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
117 if ($line=~/^\s+$/g){next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
118 my @Line=split(/\t/, $line);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
119 my $Chrom=$Line[0];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
120 my $Start=$Line[3];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
121 my $Stop=$Line[4];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
122 #my $value=$Line[5];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
123 my $ProbeName=$Line[5];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
124 my $feature="ciccio";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
125 my $check=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
126 my $relative_dist=10000000;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
127 $double_check=0;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
128 @file2=split("\n", $tab_ann{$chromosoma});
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
129 foreach $linea(@file2) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
130 chomp $linea;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
131 $linea=~ s/\#//g;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
132 my @kEle=split("\t", $linea);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
133 $ref=$kEle[$zRef];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
134 $chrom=$kEle[$zchrom];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
135 $strand=$kEle[$zstrand];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
136 $transcriptStart=$kEle[$ztxStart];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
137 $transcriptStop=$kEle[$ztxEnd];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
138 if($zcount){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
139 $exoncount=$kEle[$zcount];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
140 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
141 else
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
142 {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
143 $exoncount=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
144 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
145 $geneName=$kEle[$zname];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
146 $exonStartref=$kEle[$zexonstart];
1
78770028dcf1 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
matces
parents: 0
diff changeset
147 #my $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand";
0
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
148
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
149 my @exonStart=split(",", $exonStartref);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
150
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
151 if (!$zblocksize){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
152 $exonEndref=$kEle[$zexonend];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
153 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
154 else {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
155 @blockStop=split(",", $kEle[$zblocksize]);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
156 $exonEndref="";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
157 for ($jj=0; $jj<=$#exonStart; $jj++){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
158 $end_block=$exonStart[$jj]+$blockStop[$jj];
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
159 $exonEndref.="$end_block,";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
160
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
161 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
162 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
163
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
164 my @exonStop=split(",", $exonEndref);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
165
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
166 #print "$ref / $chrom / $strand / $transcriptStart/$transcriptStop/$exoncount/$geneName [$#exonStop]\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
167 #print "pippo $exonStart[0] - $exonStop[0],$exonStart[1] - $exonStop[1],$exonStart[2] - $exonStop[2] \n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
168
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
169
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
170 if ($Chrom eq $chrom) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
171 #print "cazzo";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
172 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
173 $promotore=$transcriptStart+$definition_pro;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
174 $distanzaTSS=int((($Start+$Stop)/2)-$transcriptStart);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
175 $trepr=$transcriptStop+$definition_tre;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
176 $rel_start=$promotore;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
177 $rel_stop=$trepr;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
178 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
179 if ($strand eq "-"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
180 $promotore=$transcriptStop-$definition_pro;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
181 $distanzaTSS=int($transcriptStop-(($Start+$Stop)/2));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
182 $trepr=$transcriptStart-$definition_tre;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
183 $rel_start=$trepr;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
184 $rel_stop=$promotore;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
185 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
186 #print OUTFILE1 "$ref\t$distanzaTSS\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
187
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
188 #if(($Start<=$transcriptStart && $Stop>$transcriptStart) || ($Start>=$promotore && $Stop<=$transcriptStart) || ($Start>=$transcriptStop && $Stop<=$promotore) || ($Start<=$promotore && $Stop>$promotore) || ($Start<$transcriptStop && $Stop>=$transcriptStop) || ($Start>=$transcriptStart && $Stop<=$transcriptStop) ){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
189 #print "sono entrato con start $Start stop $Stop e $transcriptStart e $transcriptStop\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
190
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
191 if($Start<=$rel_stop && $rel_start<=$Stop){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
192
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
193 for(my $i=0;$i<=$#exonStart;$i++) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
194
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
195 if ($strand eq "+"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
196 $exoncount1=$i+1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
197 $exoncount2=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
198 $introncount=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
199 if($i==$#exonStart) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
200 $exoncount2="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
201 $introncount="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
202 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
203 if($i==$#exonStart-1) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
204 $introncount="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
205 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
206 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
207 if ($strand eq "-"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
208 $exoncount1=($#exonStart+1)-$i;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
209 $exoncount2=$exoncount1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
210 $introncount=$exoncount1-1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
211 #if(($i==0) && ($#exonStart != 0)) {$exoncount2="last";}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
212 if($i==0) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
213 $exoncount2="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
214 $introncount="last";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
215 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
216 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
217 #print "esone start $exonStart[$i] e $exonStop[$i] e start $Start\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
218
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
219 #print OUTFILE1 "$ref\t$exonStart[$i]\t$exonStop[$i]\t$Start\t$Stop\t$i\t$#exonStart\t$priority\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
220
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
221
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
222
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
223 #if($priority eq "prom" && $check==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
224 # last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
225 #}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
226 #if($priority eq "gene" && $check==2){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
227 # next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
228 #}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
229
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
230
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
231 if(($Start<=$exonStart[$i]) && ($Stop>$exonStart[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
232 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintronexon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
233 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
234 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
235 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
236 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
237 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
238 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
239 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
240 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
241 if(($Start>=$exonStart[$i]) && ($Stop<=$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
242 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\texon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
243 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
244 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
245 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
246 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
247 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
248 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
249 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
250 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
251 if(($Start<$exonStop[$i]) && ($Stop>$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
252 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\texonintron $introncount\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
253 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
254 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
255 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
256 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
257 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
258 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
259 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
260 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
261 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
262 if(($Start>=$exonStop[$i]) && ($Stop<=$exonStart[$i+1]) && ($check==0)){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
263 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintron $introncount\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
264 #print "intron\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
265 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
266 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
267 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
268 else{
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
269 if(($Start>=$exonStop[$i]) && ($Stop<=$exonStart[$i+1])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
270 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tintron $introncount\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
271 #print "intron\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
272 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
273 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
274 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
275
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
276
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
277
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
278 if (($strand eq "+") && ($Start>=$transcriptStop)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
279 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\t3_prime\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
280 $distanzaTSS=int($transcriptStop-(($Start+$Stop)/2));
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
281 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
282 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
283 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
284 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
285 else{$check=1;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
286 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
287 if (($strand eq "-") && ($Stop<=$transcriptStart)) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
288 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\t3_prime\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
289 $distanzaTSS=int((($Start+$Stop)/2)-$transcriptStart);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
290 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
291 $check=2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
292 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
293 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
294 else{$check=1;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
295 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
296
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
297
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
298
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
299
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
300 if (($strand eq "+") && (($Start<=$promotore && $Stop>$promotore) || ($Start>$promotore && $Stop<=$transcriptStart))) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
301 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tpromoter\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
302 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
303 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
304 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
305 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
306 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
307 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
308 if (($strand eq "-") && (($Start<=$promotore && $Stop>=$promotore) || ($Start>=$transcriptStop && $Stop<$promotore))) {
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
309 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tpromoter\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
310 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
311 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
312 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
313 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
314 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
315 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
316
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
317 if(($Start<=$exonStart[$i]) && ($i==0) && ($strand eq "+") && ($Stop>=$exonStart[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
318 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tprom_exon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
319 #print "prom-exon e $exoncount1\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
320 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
321 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
322 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
323 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
324 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
325 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
326 if(($Start<=$exonStop[$i]) && ($i==$#exonStart) && ($strand eq "-") && ($Stop>=$exonStop[$i])){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
327 $feature="$ref\t$geneName\t$transcriptStart\t$transcriptStop\t$strand\t$exoncount\tprom_exon $exoncount2\t$distanzaTSS";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
328 if($priority eq "prom"){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
329 $check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
330 #last;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
331 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
332 else{$check=2;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
333 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
334
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
335 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
336 #if ($check==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
337 # print "$chrom\t$Start\t$Stop\t$geneName\t$exoncount\t$ref\t$strand\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
338 #}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
339 }else{next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
340 #exit;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
341 }else{next;}
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
342
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
343 #print OUTFILE1 "$ref\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
344 #print "$geneName\t$transcriptStart\t$Chrom\t$Start\t$Stop\t$distanzaTSS\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
345
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
346 if (($priority eq "gene") && ($relative_dist>abs($distanzaTSS))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
347 $relative_dist=abs($distanzaTSS);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
348 $stampa="$Chrom\t$Start\t$Stop\t$ProbeName\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
349 $double_check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
350 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
351 if (($check==1) && ($priority eq "prom") && ($relative_dist>abs($distanzaTSS))){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
352 $relative_dist=abs($distanzaTSS);
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
353 $double_check=1;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
354 $stampa="$Chrom\t$Start\t$Stop\t$ProbeName\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
355 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
356 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
357
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
358
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
359
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
360 if($double_check==1){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
361 print OUTFILE1 "$stampa";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
362 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
363 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
364 if (($check==2) && ($priority eq "prom")){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
365 print OUTFILE1 "$Chrom\t$Start\t$Stop\t$ProbeName\t$feature\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
366 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
367 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
368 if($check==0){
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
369 print OUTFILE1 "$Chrom\t$Start\t$Stop\t$ProbeName\tintergenic\tintergenic\t$Start\t$Stop\t+\t0\tOUT\t$definition_out\n";
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
370 next;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
371 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
372 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
373 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
374 close INFILE;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
375 close INFILE2;
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
376 }
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
377
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
378
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
379
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
380
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
381
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
382
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
383
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
384
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
385
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
386
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
387
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
388
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
389
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
390
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
391
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
392
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
393
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
394
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
395
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
396
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
397
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
398
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
399
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
400
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
401
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
402
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
403
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
404
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
405
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
406
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
407
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
408
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
409
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
410
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
411
cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
matces
parents:
diff changeset
412