From 40da90ab803586a828ec3e11c4f643d3748a41a6 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Fri, 28 Jun 2024 14:42:37 +0200
Subject: [PATCH 1/2] fix #420. Now table 0 can be called (bioperl >= april
 2024 must be present). Fix issue in get_proper_codon_table. Force
 agat_sp_extract_sequences.pl to pass by the get_proper_codon_table (the only
 one that was not yet using it). Add an explanation section Troubleshooting of
 the doc

---
 bin/agat_sp_add_start_and_stop.pl             |  2 +-
 bin/agat_sp_extract_sequences.pl              |  8 +--
 ...sp_filter_incomplete_gene_coding_models.pl |  2 +-
 bin/agat_sp_fix_fusion.pl                     |  1 -
 bin/agat_sp_fix_longest_ORF.pl                |  1 -
 ...agat_sp_fix_small_exon_from_extremities.pl |  2 +-
 bin/agat_sp_flag_premature_stop_codons.pl     |  5 +-
 ..._prokka_fix_fragmented_gene_annotations.pl |  1 -
 docs/troubleshooting.md                       | 64 ++++++++++++++++++-
 lib/AGAT/Utilities.pm                         | 15 +++--
 10 files changed, 81 insertions(+), 20 deletions(-)

diff --git a/bin/agat_sp_add_start_and_stop.pl b/bin/agat_sp_add_start_and_stop.pl
index 20548571..8dd93004 100755
--- a/bin/agat_sp_add_start_and_stop.pl
+++ b/bin/agat_sp_add_start_and_stop.pl
@@ -66,7 +66,7 @@
 my $gffout = prepare_gffout($config, $opt_output);
 
 $codon_table_id = get_proper_codon_table($codon_table_id);
-print "Codon table ".$codon_table_id." in use. You can change it using --table option.\n";
+
 my $codon_table = Bio::Tools::CodonTable->new( -id => $codon_table_id, -no_iupac => 0);
 # #####################################
 # # END Manage OPTION
diff --git a/bin/agat_sp_extract_sequences.pl b/bin/agat_sp_extract_sequences.pl
index dca93b8e..706818a4 100755
--- a/bin/agat_sp_extract_sequences.pl
+++ b/bin/agat_sp_extract_sequences.pl
@@ -96,6 +96,9 @@
 # --- Manage config ---
 $config = get_agat_config({config_file_in => $config});
 
+# --- Check codon table
+$codonTable = get_proper_codon_table($codonTable);
+
 # activate warnings limit
 my %warnings;
 activate_warning_limit(\%warnings, 10);
@@ -121,11 +124,6 @@
 print "We will extract the $opt_type sequences.\n";
 $opt_type=lc($opt_type);
 
-# deal with codon table
-if($codonTable<0 and $codonTable>25){
-  print "$codonTable codon table is not a correct value. It should be between 0 and 25 (0,23 and 25 can be problematic !)\n";
-}
-
 # deal with OFS
 my $OFS=" ";
 if($opt_OFS){
diff --git a/bin/agat_sp_filter_incomplete_gene_coding_models.pl b/bin/agat_sp_filter_incomplete_gene_coding_models.pl
index 0234e370..d0c2a340 100755
--- a/bin/agat_sp_filter_incomplete_gene_coding_models.pl
+++ b/bin/agat_sp_filter_incomplete_gene_coding_models.pl
@@ -61,7 +61,7 @@
 
 # --- Check codon table ---
 $codonTableId = get_proper_codon_table($codonTableId);
-print "Codon table ".$codonTableId." in use. You can change it using --table option.\n";
+
 my $codonTable = Bio::Tools::CodonTable->new( -id => $codonTableId);
 
 ######################
diff --git a/bin/agat_sp_fix_fusion.pl b/bin/agat_sp_fix_fusion.pl
index 52277325..b716e1c8 100755
--- a/bin/agat_sp_fix_fusion.pl
+++ b/bin/agat_sp_fix_fusion.pl
@@ -87,7 +87,6 @@
 my $logout = prepare_fileout($logout_file);
 
 $opt_codonTableID = get_proper_codon_table($opt_codonTableID);
-print "Codon table ".$opt_codonTableID." in use. You can change it using --table option.\n";
 
 if(!$threshold){
   $threshold=100;
diff --git a/bin/agat_sp_fix_longest_ORF.pl b/bin/agat_sp_fix_longest_ORF.pl
index 6fddecbe..ea797d97 100755
--- a/bin/agat_sp_fix_longest_ORF.pl
+++ b/bin/agat_sp_fix_longest_ORF.pl
@@ -72,7 +72,6 @@
 
 # --- Check codon table
 $codonTable = get_proper_codon_table($codonTable);
-print "Codon table ".$codonTable." in use. You can change it using --table option.\n";
 
 ######################
 # Manage output file #
diff --git a/bin/agat_sp_fix_small_exon_from_extremities.pl b/bin/agat_sp_fix_small_exon_from_extremities.pl
index 13799c01..82cc983d 100755
--- a/bin/agat_sp_fix_small_exon_from_extremities.pl
+++ b/bin/agat_sp_fix_small_exon_from_extremities.pl
@@ -61,8 +61,8 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    EXTRA     <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# --- Check codon table
 $codonTableId = get_proper_codon_table($codonTableId);
-print "Codon table ".$codonTableId." in use. You can change it using --table option.\n";
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     MAIN     <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
diff --git a/bin/agat_sp_flag_premature_stop_codons.pl b/bin/agat_sp_flag_premature_stop_codons.pl
index d7e4f248..500a8bd7 100755
--- a/bin/agat_sp_flag_premature_stop_codons.pl
+++ b/bin/agat_sp_flag_premature_stop_codons.pl
@@ -26,7 +26,7 @@
                 	'o|out|output=s'    => \$opt_output,
 					"fasta|fa|f=s"      => \$file_fasta,
 					"table|codon|ct=i"  => \$codonTable,
-                 	'c|config=s'               => \$config,
+                 	'c|config=s'        => \$config,
                  	'h|help!'           => \$opt_help ) )
 {
     pod2usage( { -message => 'Failed to parse command line',
@@ -53,6 +53,9 @@
 # --- Manage config ---
 $config = get_agat_config({config_file_in => $config});
 
+# --- Check codon table
+$codonTable = get_proper_codon_table($codonTable);
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    PARAMS    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 my $ostreamReport_file;
diff --git a/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl b/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl
index ff8cd8bd..84d7cb67 100755
--- a/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl
+++ b/bin/agat_sp_prokka_fix_fragmented_gene_annotations.pl
@@ -114,7 +114,6 @@ BEGIN
 
 # Check codon table
 $codonTable = get_proper_codon_table($codonTable);
-print "Codon table ".$codonTable." in use. You can change it using --table option.\n";
 
 ######################
 # Manage output file #
diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md
index 1e88cd05..954c12ec 100644
--- a/docs/troubleshooting.md
+++ b/docs/troubleshooting.md
@@ -75,4 +75,66 @@ Bio::DB::Fasta from Bioperl cannot handle line with more than 65,536 characters.
 # Fold to 80 characters by line. 
 # Be careful if you have long headers that can be folded over several lines. You must first shorten them, or fold with higher value.
 fold input.fa > output.fa
-```
\ No newline at end of file
+```
+
+
+## How to use codon table 0 (codon table 1 is used instead)?
+
+Several scripts need to use a codon table:
+
+```
+agat_sp_add_start_and_stop.pl  
+agat_sp_extract_sequences.pl  
+agat_sp_filter_incomplete_gene_coding_models.pl  
+agat_sp_fix_fusion.pl
+agat_sp_fix_longest_ORF.pl
+agat_sp_fix_small_exon_from_extremities.pl
+agat_sp_flag_premature_stop_codons.pl
+agat_sp_prokka_fix_fragmented_gene_annotations.pl
+```
+
+By default AGAT uses codon table 1 wich is the standard table. 
+
+* What is the difference between table 1 and table 0?  
+  The codon table 0 is strict and uses ATG-only start codon, while codon table 1 uses TTG, CTG and ATG possible start codon.
+
+* What are the possible codon table?   
+  In top of the table 0 which is specific to Bioperl many other tables are available. Their description can be found [here](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1).
+
+## Why when asking for table 0 AGAT keep using the table 1 ?
+
+There are two possible reasons for that problem.
+
+  * AGAT: Originally the problem comes from a bug in Bioperl. AGAT was trying to pass by the problem but the fix was not efficient until version 1.4.1. Please be sure to use a version >= 1.4.1 to avoid any problem from the AGAT side.
+
+  * Bioperl: The problem has been present for a while and has been definitly fixed in the [commit fa9366f from the 24th of April 2024](https://github.com/bioperl/bioperl-live/tree/fa9366f3a2f48fd051343d488cfce26655f842b3).  
+  So to fix the problem you need to use a bioperl version equal or later to that point. If not possible (e.g. not yet available for installation via conda) you can follow this procedure:
+      * run AGAT once
+      * catch the location of bioperl used from the prompt e.g.:
+        ```
+         ------------------------------------------------------------------------------
+        |   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+        |   https://github.com/NBISweden/AGAT                                          |
+        |   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+        ------------------------------------------------------------------------------
+        
+        ...
+
+        => Machine information:
+              This script is being run by perl v5.32.1
+              Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/
+              Operating system being used: linux
+        ```
+        Here the bioperl path is here: `/usr/local/lib/perl5/site_perl/Bio/`
+      * Move into the directory found in the previous step minus `/Bio`:
+        `cd /usr/local/lib/perl5/site_perl/`
+      * Copy paste locally the file and the folder from the bioperl-live repository (here)[https://github.com/bioperl/bioperl-live/tree/master/lib]:  
+        ```
+        git clone https://github.com/bioperl/bioperl-live
+        cp -r bioperl-live/lib/* .
+        ```
+        
+      Now you should be able to use the codon table 0. If not check your AGAT version (see above).
+
+
+
diff --git a/lib/AGAT/Utilities.pm b/lib/AGAT/Utilities.pm
index 156d04e5..d1a91455 100644
--- a/lib/AGAT/Utilities.pm
+++ b/lib/AGAT/Utilities.pm
@@ -76,19 +76,20 @@ sub get_proper_codon_table {
   my ($codon_table_id_original) = @_;
   my $codonTable = Bio::Tools::CodonTable->new( -id => $codon_table_id_original);
   my $codon_table_id_bioperl = $codonTable->id;
-  if (!$codon_table_id_bioperl){
-	$codon_table_id_bioperl = 1 ;
-	$codonTable = Bio::Tools::CodonTable->new( -id => $codon_table_id_original);
-  }  
+  
+  # To deal with empty result in version of bioperl < april 2024 when asking with table 0 (it was reutrning an empty string)
+  if (! defined($codon_table_id_bioperl)){
+	$codon_table_id_bioperl = 1 ; # default codon table
+  }
 
   if ($codon_table_id_original == 0 and  $codon_table_id_original != $codon_table_id_bioperl){
     $codonTable->warn("Your version of bioperl do not handle codon table 0\n".
     "see https://github.com/bioperl/bioperl-live/pull/315\n".
     "It uses codon table $codon_table_id_bioperl instead.");
-    return $codon_table_id_bioperl;
   }
-
-  return $codon_table_id_original;
+  
+  print "Codon table ".$codon_table_id_bioperl." in use. You can change it using the appropriate parameter.\n";
+  return $codon_table_id_bioperl;
 }
 
 # the warning message will be filtered to be printed only $nb_warnings times

From c2ff6a4cea5faaf9bd92b7a85e80c19cb01f41a1 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Fri, 28 Jun 2024 16:39:10 +0200
Subject: [PATCH 2/2] increment AGAT version

---
 lib/AGAT/AGAT.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/AGAT/AGAT.pm b/lib/AGAT/AGAT.pm
index 8d757a7b..e7b6b9e4 100644
--- a/lib/AGAT/AGAT.pm
+++ b/lib/AGAT/AGAT.pm
@@ -16,7 +16,7 @@ use AGAT::Utilities;
 use AGAT::PlotR;
 use Bio::Tools::GFF;
 
-our $VERSION     = "v1.4.0";
+our $VERSION     = "v1.4.1";
 our @ISA         = qw(Exporter);
 our @EXPORT      = qw(get_agat_header print_agat_version get_agat_config handle_levels);
 sub import {