diff Haplophyle.pl @ 0:6f11162b6fa2 draft

planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Haplophyle.pl	Tue Aug 14 08:04:23 2018 -0400
@@ -0,0 +1,142 @@
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+use Bio::SeqIO;
+
+use Cwd;
+my $dir = getcwd;
+
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input>
+    -o, --output        <output>
+    -d, --dotfile       <dotfile>
+<opts> are:
+    -g, --groups        <groupfile>
+    -s, --stats         <statfile>
+    -t, --tool_path     <tool_path>
+~;
+$usage .= "\n";
+
+my ($infile,$output,$outfile,$groupfile,$statfile,$tool_path);
+
+
+GetOptions(
+	"input=s"    => \$infile,
+	"output=s"   => \$output,
+	"dot=s"      => \$outfile,
+	"groups=s"   => \$groupfile,
+	"stats=s"    => \$statfile,
+	"tool_path=s"=> \$tool_path
+);
+
+
+die $usage
+  if ( !$infile);
+
+
+my $HAPLOPHYLE_EXE = "java -Xmx2048m -jar NetworkCreator_fat.jar";
+if ($tool_path){
+	$HAPLOPHYLE_EXE = "java -Xmx2048m -jar $tool_path/NetworkCreator_fat.jar";
+}
+  
+	
+my $out_png = "network.png";
+
+my $command = "$HAPLOPHYLE_EXE -in $infile -out $outfile";
+system($command);
+
+
+
+my %groups;
+my %groups2;
+my %hash;
+my %haplosize;
+if ($groupfile && $statfile){
+	open(G,$groupfile);
+	while(<G>){
+		my $line = $_;$line=~s/\n//g;$line=~s/\r//g;
+		my ($ind,$group) = split(";",$line);
+		if ($group =~/\w+/ && $ind=~/\w+/){
+			$groups{$group}.=$ind.",";	
+			$groups2{$ind} = $group;
+		}
+	}
+	close(G);
+
+	open(S,$statfile);
+	while(<S>){
+		if (/^(haplo\d+):(\d+):(.*)/){
+			my $haplo_num = $1;
+			my $nb_haplo = $2;
+			my $inds = $3;
+			my @inds = split(",",$3);
+			foreach my $ind(@inds){
+				my ($indname,$rank) = split("_",$ind);
+				my $group = $groups2{$indname};
+				$hash{$haplo_num}{$group}++;
+				$haplosize{$haplo_num}++;
+			}
+		}
+	}
+	close(S);	
+}
+
+my $nb_groups = scalar keys(%groups);
+my @colors = ("#ed292a","#ed292a","#82ABA0","#2255a6","#6ebe43","#e76599","#662e91","#c180ff","#ea8b2f","#fff100","#666666","#01ffff","#bfbfbf","#2ac966","#666666");
+my $pie_block = "";
+my %correspondence_groups;
+my $i = 0;
+foreach my $group(keys(%groups)){
+	$i++;
+	$correspondence_groups{$i} = $group;
+	$pie_block .= "'pie-$i-background-color': '$colors[$i]',\n";
+	$pie_block .= "'pie-$i-background-size': 'mapData(group$i, 0, 10, 0, 100)',\n";
+}
+open(JSON_CYTOSCAPE,">$output");
+my $json = "{\"elements\": {\"nodes\": [";
+my $done = 0;
+open(OUTFILE,"$outfile");
+while(<OUTFILE>){
+                        if (/(^\w+)\s\[.*width=([\d\.]+),/){
+                                my $node = $1;
+                                my $size = $2;
+                               	my $ref_hash = $hash{$node};
+                                if ($ref_hash){
+                                        my %hash2 = %$ref_hash;
+                                        my $s = scalar keys(%hash2);
+					$json.= "{ \"data\": { \"id\": \"$node\", \"width\": $size";
+                                        for (my $i = 1; $i <= $nb_groups; $i++){
+						my $group = $correspondence_groups{$i};
+						my $ratio = 0;
+						if ($haplosize{$node} > 0 && $hash{$node}{$group} > 0){	
+	                                                $ratio = ($hash{$node}{$group}/$haplosize{$node}) * 10;
+						}
+						$json .= ", group$i: $ratio";
+                                        }
+					$json.= " } },\n";
+                                }
+                                else{
+					$json.= "{ \"data\": { \"id\": \"$node\", \"width\": $size} },\n";
+                                }
+                        }
+                        if (/(\w+) -- (\w+)/){
+                                if ($done == 0){
+                                        $done = 1;
+					chop($json);
+					chop($json);
+					$json .= "],\n";
+					$json .= "\"edges\": [\n";
+                                }
+                                $done = 1;
+				$json.= "{ \"data\": { \"id\": \"$1$2\", \"weight\": 1, \"source\": \"$1\", \"target\": \"$2\"} },\n";
+                        }
+}
+chop($json);
+chop($json);
+$json.="]}}";
+print JSON_CYTOSCAPE $json;
+close(JSON_CYTOSCAPE);
+