From f165286b98fd1e674f571e00a2a953769b79c784 Mon Sep 17 00:00:00 2001
From: KatharinaHoff <katharina.hoff@gmail.com>
Date: Sat, 23 Dec 2023 19:01:57 +0100
Subject: [PATCH] moving best_by_compleasm output files

---
 scripts/braker.pl | 53 +++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 51 insertions(+), 2 deletions(-)

diff --git a/scripts/braker.pl b/scripts/braker.pl
index fd70eab..ae1e107 100755
--- a/scripts/braker.pl
+++ b/scripts/braker.pl
@@ -9950,8 +9950,57 @@ sub best_by_compleasm {
     system("$cmdStr") == 0
             or die("ERROR in file " . __FILE__ ." at line ". __LINE__
             . "\nFailed to execute: $cmdStr\n");
-    if(-e "$otherfilesDir/better.gtf"){
-
+    open(CLOG, "<", "$otherfilesDir/best_by_compleasm.log") or die("ERROR in file "
+        . __FILE__ . " at line " . __LINE__
+        . "\nCould not open file $otherfilesDir/best_by_compleasm.log!\n");
+    my $last_line;
+    $last_line = $_ while (<CLOG>);  # Read in the last line.
+    close(CLOG) or die("ERROR in file "
+        . __FILE__ . " at line " . __LINE__
+        . "\nCould not close file $otherfilesDir/best_by_compleasm.log!\n");
+    if($last_line =! m/braker\.gtf/){
+        print LOG "\# " . (localtime) . ": best gene set found by compleasm "
+            . "is not the original braker gene set.\n" if ($v > 2);
+        # create a directory $otherfilesDir/braker_original
+        mkdir("$otherfilesDir/braker_original") or die("ERROR in file "
+            . __FILE__ . " at line " . __LINE__
+            . "\nCould not create directory $otherfilesDir/braker_original!\n");
+        # mv $otherfilesDir/braker.gtf to $otherfilesDir/braker_original/braker.gtf
+        $cmdStr = "mv $otherfilesDir/braker.gtf $otherfilesDir/braker_original/braker.gtf";
+        print LOG "\# " . (localtime) . ": $cmdStr\n" if ($v > 2);
+        system("$cmdStr") == 0
+            or die("ERROR in file " . __FILE__ ." at line ". __LINE__
+            . "\nFailed to execute: $cmdStr\n");
+        # mv $otherfilesDir/braker.aa to $otherfilesDir/braker_original/braker.aa
+        $cmdStr = "mv $otherfilesDir/braker.aa $otherfilesDir/braker_original/braker.aa";
+        print LOG "\# " . (localtime) . ": $cmdStr\n" if ($v > 2);
+        system("$cmdStr") == 0
+            or die("ERROR in file " . __FILE__ ." at line ". __LINE__
+            . "\nFailed to execute: $cmdStr\n");
+        # mv $otherfilesDir/braker.codingseq to $otherfilesDir/braker_original/braker.codingseq
+        $cmdStr = "mv $otherfilesDir/braker.codingseq $otherfilesDir/braker_original/braker.codingseq";
+        print LOG "\# " . (localtime) . ": $cmdStr\n" if ($v > 2);
+        system("$cmdStr") == 0
+            or die("ERROR in file " . __FILE__ ." at line ". __LINE__
+            . "\nFailed to execute: $cmdStr\n");
+        # mv $otherfilesDir/bbc/better.gtf to $otherfilesDir/braker.gtf
+        $cmdStr = "mv $otherfilesDir/bbc/better.gtf $otherfilesDir/braker.gtf";
+        print LOG "\# " . (localtime) . ": $cmdStr\n" if ($v > 2);
+        system("$cmdStr") == 0
+            or die("ERROR in file " . __FILE__ ." at line ". __LINE__
+            . "\nFailed to execute: $cmdStr\n");
+        # mv $otherfilesDir/bbc/better.aa to $otherfilesDir/braker.aa
+        $cmdStr = "mv $otherfilesDir/bbc/better.aa $otherfilesDir/braker.aa";
+        print LOG "\# " . (localtime) . ": $cmdStr\n" if ($v > 2);
+        system("$cmdStr") == 0
+            or die("ERROR in file " . __FILE__ ." at line ". __LINE__
+            . "\nFailed to execute: $cmdStr\n");
+        # mv $otherfilesDir/bbc/better.codingseq to $otherfilesDir/braker.codingseq
+        $cmdStr = "mv $otherfilesDir/bbc/better.codingseq $otherfilesDir/braker.codingseq";
+        print LOG "\# " . (localtime) . ": $cmdStr\n" if ($v > 2);
+        system("$cmdStr") == 0
+            or die("ERROR in file " . __FILE__ ." at line ". __LINE__
+            . "\nFailed to execute: $cmdStr\n");
     }
 }