Merge branch 'master' of github.com:TransDecoder/TransDecoder into devel

brianjohnhaas · brianjohnhaas · commit 701fbf912488 · 2023-01-27T16:46:07.000Z
diff --git a/Changelog.txt b/Changelog.txt
@@ -1,3 +1,15 @@
+## v5.6.0, Apr 07, 2022
+- genome propagation of orfs resets orientation for unspliced transcripts with opposite strand orfs.
+- speed update from Yanick Paco Hagemeijer
+- added option --output_dir | -O  to both TransDecoder.LongOrfs and TransDecoder.Predict, as per request, so users can point to specific output directories rather than relying on the default ( basename(target.fasta) + ".transdecoder_dir/").
+- removing track name from bed output
+- if select single best orf, do selection before removing overlapping preds
+- updated get_longest_ORF_per_transcript.pl to match current header formatting
+- really retain all blast hits, ignoring overlaps to prev selected entries, unless single_best_orf indicated
+- updated genetic code options in help menu
+
+
+
 ## v5.5.0, Oct 22, 2018
 added option --output_dir | -O  to both TransDecoder.LongOrfs and TransDecoder.Predict, as per request, so users can point to specific output directories rather than relying on the default ( basename(target.fasta) + ".transdecoder_dir/").
 
diff --git a/TransDecoder.LongOrfs b/TransDecoder.LongOrfs
@@ -21,7 +21,7 @@ use Pipeliner;
 
 
 #my $VERSION = "__BLEEDING_EDGE__";
-my $VERSION = "5.5.0";
+my $VERSION = "5.6.0";
 
 my $UTIL_DIR = "$FindBin::RealBin/util";
 $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
diff --git a/TransDecoder.Predict b/TransDecoder.Predict
@@ -23,7 +23,7 @@ use DelimParser;
 
 
 #my $VERSION = "__BLEEDING_EDGE__";
-my $VERSION = "5.5.0";
+my $VERSION = "5.6.0";
 
 my $RETAIN_LONG_ORFS_MIN_LENGTH = 1000000; # so essentially, off by default
 
diff --git a/util/get_longest_ORF_per_transcript.pl b/util/get_longest_ORF_per_transcript.pl
@@ -21,7 +21,6 @@
 
          #  
          #  len:365 (+) asmbl_104:2-1096(+)
-         #  
 
          if ($header =~ /len:(\d+) .* (\S+):\d+-\d+\([+-]\)/) {
              my $len = $1;

Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,6 @@`
`21`	`21`
`22`	`22`	`#`
`23`	`23`	`# len:365 (+) asmbl_104:2-1096(+)`
`24`		`- #`
`25`	`24`
`26`	`25`	`if ($header =~ /len:(\d+) .* (\S+):\d+-\d+\([+-]\)/) {`
`27`	`26`	`my $len = $1;`