Mercurial > repos > dereeper > haplophyle
annotate Haplophyle.pl @ 0:6f11162b6fa2 draft
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author | dereeper |
---|---|
date | Tue, 14 Aug 2018 08:04:23 -0400 |
parents | |
children | 8e248dc6ad56 |
rev | line source |
---|---|
0
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
1 #!/usr/bin/perl |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
2 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
3 use strict; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
4 use Getopt::Long; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
5 use Bio::SeqIO; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
6 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
7 use Cwd; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
8 my $dir = getcwd; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
9 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
10 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
11 my $usage = qq~Usage:$0 <args> [<opts>] |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
12 where <args> are: |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
13 -i, --input <input> |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
14 -o, --output <output> |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
15 -d, --dotfile <dotfile> |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
16 <opts> are: |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
17 -g, --groups <groupfile> |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
18 -s, --stats <statfile> |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
19 -t, --tool_path <tool_path> |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
20 ~; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
21 $usage .= "\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
22 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
23 my ($infile,$output,$outfile,$groupfile,$statfile,$tool_path); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
24 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
25 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
26 GetOptions( |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
27 "input=s" => \$infile, |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
28 "output=s" => \$output, |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
29 "dot=s" => \$outfile, |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
30 "groups=s" => \$groupfile, |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
31 "stats=s" => \$statfile, |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
32 "tool_path=s"=> \$tool_path |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
33 ); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
34 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
35 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
36 die $usage |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
37 if ( !$infile); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
38 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
39 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
40 my $HAPLOPHYLE_EXE = "java -Xmx2048m -jar NetworkCreator_fat.jar"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
41 if ($tool_path){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
42 $HAPLOPHYLE_EXE = "java -Xmx2048m -jar $tool_path/NetworkCreator_fat.jar"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
43 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
44 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
45 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
46 my $out_png = "network.png"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
47 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
48 my $command = "$HAPLOPHYLE_EXE -in $infile -out $outfile"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
49 system($command); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
50 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
51 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
52 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
53 my %groups; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
54 my %groups2; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
55 my %hash; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
56 my %haplosize; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
57 if ($groupfile && $statfile){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
58 open(G,$groupfile); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
59 while(<G>){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
60 my $line = $_;$line=~s/\n//g;$line=~s/\r//g; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
61 my ($ind,$group) = split(";",$line); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
62 if ($group =~/\w+/ && $ind=~/\w+/){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
63 $groups{$group}.=$ind.","; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
64 $groups2{$ind} = $group; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
65 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
66 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
67 close(G); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
68 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
69 open(S,$statfile); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
70 while(<S>){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
71 if (/^(haplo\d+):(\d+):(.*)/){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
72 my $haplo_num = $1; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
73 my $nb_haplo = $2; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
74 my $inds = $3; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
75 my @inds = split(",",$3); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
76 foreach my $ind(@inds){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
77 my ($indname,$rank) = split("_",$ind); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
78 my $group = $groups2{$indname}; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
79 $hash{$haplo_num}{$group}++; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
80 $haplosize{$haplo_num}++; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
81 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
82 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
83 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
84 close(S); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
85 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
86 |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
87 my $nb_groups = scalar keys(%groups); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
88 my @colors = ("#ed292a","#ed292a","#82ABA0","#2255a6","#6ebe43","#e76599","#662e91","#c180ff","#ea8b2f","#fff100","#666666","#01ffff","#bfbfbf","#2ac966","#666666"); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
89 my $pie_block = ""; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
90 my %correspondence_groups; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
91 my $i = 0; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
92 foreach my $group(keys(%groups)){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
93 $i++; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
94 $correspondence_groups{$i} = $group; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
95 $pie_block .= "'pie-$i-background-color': '$colors[$i]',\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
96 $pie_block .= "'pie-$i-background-size': 'mapData(group$i, 0, 10, 0, 100)',\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
97 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
98 open(JSON_CYTOSCAPE,">$output"); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
99 my $json = "{\"elements\": {\"nodes\": ["; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
100 my $done = 0; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
101 open(OUTFILE,"$outfile"); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
102 while(<OUTFILE>){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
103 if (/(^\w+)\s\[.*width=([\d\.]+),/){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
104 my $node = $1; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
105 my $size = $2; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
106 my $ref_hash = $hash{$node}; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
107 if ($ref_hash){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
108 my %hash2 = %$ref_hash; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
109 my $s = scalar keys(%hash2); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
110 $json.= "{ \"data\": { \"id\": \"$node\", \"width\": $size"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
111 for (my $i = 1; $i <= $nb_groups; $i++){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
112 my $group = $correspondence_groups{$i}; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
113 my $ratio = 0; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
114 if ($haplosize{$node} > 0 && $hash{$node}{$group} > 0){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
115 $ratio = ($hash{$node}{$group}/$haplosize{$node}) * 10; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
116 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
117 $json .= ", group$i: $ratio"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
118 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
119 $json.= " } },\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
120 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
121 else{ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
122 $json.= "{ \"data\": { \"id\": \"$node\", \"width\": $size} },\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
123 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
124 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
125 if (/(\w+) -- (\w+)/){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
126 if ($done == 0){ |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
127 $done = 1; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
128 chop($json); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
129 chop($json); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
130 $json .= "],\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
131 $json .= "\"edges\": [\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
132 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
133 $done = 1; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
134 $json.= "{ \"data\": { \"id\": \"$1$2\", \"weight\": 1, \"source\": \"$1\", \"target\": \"$2\"} },\n"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
135 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
136 } |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
137 chop($json); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
138 chop($json); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
139 $json.="]}}"; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
140 print JSON_CYTOSCAPE $json; |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
141 close(JSON_CYTOSCAPE); |
6f11162b6fa2
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
dereeper
parents:
diff
changeset
|
142 |