Version display (#353)

* clean printed message and add AGAT header to know which version is ran --------- Co-authored-by: Jacques Dainat <jacques.dainat@ird.fr>
NBISweden · Apr 25, 2023 · f07ca0b · f07ca0b
1 parent d613f0e
commit f07ca0b
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Showing 2 changed files with 17 additions and 8 deletions.
diff --git a/lib/AGAT/OmniscientI.pm b/lib/AGAT/OmniscientI.pm
@@ -118,7 +118,7 @@ sub slurp_gff3_file_JD {
 	# +----------------- Check we receive a hash as ref ------------------+
 	if(ref($args) ne 'HASH'){ print "Hash Arguments expected for slurp_gff3_file_JD. Please check the call.\n"; exit;	}
 
-	#  +-----------------  Declare all variables and fill them ------------------+
+	# +-----------------  Declare all variables and fill them ------------------+
 	my ( $file, $gff_in_format, $locus_tag, $verbose, $merge_loci,
 	    $log, $debug, $throw_fasta, $progress_bar);
 
@@ -148,13 +148,15 @@ sub slurp_gff3_file_JD {
 			my $log_name = $filename.".agat.log";
 			open($log, '>', $log_name  ) or
 						dual_print($log, "Can not open $log_name for printing: $!", 1) && die;
-			print $log AGAT::AGAT::get_agat_header(); # print AGAT header
 			print $log file_text_line({ string => (strftime "%m/%d/%Y at %Hh%Mm%Ss", localtime),
 																  char => " ",
 																  extra => "\n"});
 		}
 	}
 
+	# +----------------- Print header ------------------+
+	dual_print ($log, AGAT::AGAT::get_agat_header(), $verbose);
+
 	# +----------------- debug param  ------------------+
 	$debug = $config->{debug};
 
@@ -175,7 +177,8 @@ sub slurp_gff3_file_JD {
 	$throw_fasta = $config->{throw_fasta};
 
 	# +---------------------------------- Write header info  ----------------------------------+
-	dual_print ($log, surround_text("- Start parsing -",80,"*"), $verbose);
+	dual_print ($log,sizedPrint("\n",80, "\n"), $verbose);
+	dual_print ($log,sizedPrint("------ Start parsing ------",80, "\n"), $verbose);
 	dual_print ($log, file_text_line({ string => "parse options and metadata", char => "-" }), $verbose);
 
 	# +-- load files --+
@@ -405,7 +408,7 @@ sub slurp_gff3_file_JD {
 	}
 
 	# Parsing time
-	dual_print ($log, surround_text("- End parsing -\ndone in ".(time() - $start_run)." seconds",80,"*","\n"), $verbose );
+	dual_print ($log,sizedPrint("------ End parsing (done in ".(time() - $start_run)." second) ------",80, "\n\n\n"), $verbose);
 	$previous_time = time();
 	my $check_time = $previous_time;
 
@@ -415,7 +418,7 @@ sub slurp_gff3_file_JD {
 
 	# -------------------- Mandatory checks --------------------
 	my $check_cpt = 1;
-	dual_print ($log, surround_text("- Start checks -",80,"*"), $verbose);
+	dual_print ($log,sizedPrint("------ Start checks ------",80, "\n"), $verbose);
 
 	dual_print ($log, file_text_line({ string => "Check$check_cpt: feature types", char => "-" }), $verbose );
 	_handle_globalWARNS({ warning => \%globalWARNS, ontology => $ontology, log => $log, type => "ontology", verbose => $verbose });
@@ -544,9 +547,7 @@ sub slurp_gff3_file_JD {
 		}
 	}
 
-	dual_print ($log, surround_text("- End checks -\ndone in ".(time() - $check_time)." seconds",80,"*","\n"), $verbose );
-
- dual_print ($log, "=> OmniscientI total time: ".(time() - $start_run)." seconds\n", $verbose );
+	dual_print ($log,sizedPrint("------ End checks (done in ".(time() - $check_time)." second) ------",80, "\n\n\n"), $verbose);
 
 	#return
 	return \%omniscient, \%mRNAGeneLink	;

diff --git a/lib/AGAT/Utilities.pm b/lib/AGAT/Utilities.pm
@@ -116,6 +116,11 @@ sub activate_warning_limit{
 #               Char (character to use to make the frame),
 #								String (extra to print at the end after the frame)
 # @output 1 => String
+#e.g. surround_text("- Start parsing -",80,"*")
+#  ********************************************************************************
+#  *                              - Start parsing -                               *
+#  ********************************************************************************
+#
 sub surround_text{
   my ($term, $size, $char, $extra) = @_;
 
@@ -156,6 +161,9 @@ sub surround_text{
 	return $result;
 }
 
+# e.g.  file_text_line({ string => "parse options and metadata", char => "-" })
+# -------------------------- parse options and metadata --------------------------
+#
 sub file_text_line{
   my ($args) = @_;