20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,95 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Cwd;
+use File::Basename;
+
+my $usage = "usage: $0 cNumb.graph\n\n";
+
+my $comp = $ARGV[0] or die $usage;
+
+my $TRINITY_HOME = $ENV{TRINITY_HOME} or die "Error, need env var TRINITY_HOME";
+
+main: {
+
+
+    my $base_comp_name = basename($comp);
+    
+    my $cwd = cwd();
+
+    unless ($comp =~ /^\//) {
+        $comp = "$cwd/$comp";
+        
+    }
+
+    
+    
+    
+    { ## run old butterfly
+        
+        my $workdir = "$cwd/__$base_comp_name.oldBfly_dir";
+
+        mkdir($workdir) or die "Error, cannot mkdir $workdir";
+        chdir $workdir or die $!;
+     
+        my $cmd = "ln -s $comp.reads .;  ln -s $comp.out .";
+        &process_cmd($cmd);
+
+        $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/prev_vers/Butterfly_r2013_08_14.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
+
+        open (my $ofh, ">bfly.cmd") or die $!;
+        print $ofh $cmd;
+        close $ofh;
+
+        &process_cmd($cmd);
+
+    }
+    
+    chdir $cwd or die $!;
+
+    
+    { ## run new butterfly
+
+        my $workdir = "$cwd/__$base_comp_name.newBfly_dir";
+        
+        mkdir($workdir) or die $!;
+        chdir ($workdir) or die $!;
+
+        my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
+        &process_cmd($cmd);
+        
+
+        $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
+
+        open (my $ofh, ">bfly.cmd") or die $!;
+        print $ofh $cmd;
+        close $ofh;
+
+
+        &process_cmd($cmd);
+
+
+    }
+
+
+    exit(0);
+}
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    my $ret = system($cmd);
+    
+    if ($ret) {
+        die "Error, CMD: $cmd died with ret $ret";
+    }
+
+    return;
+}
+
+