Config file can now be called as you wish and located where you want (#…

…376) * change config.yaml by agat_config.yaml * add config option (can be called and located anywhere)
NBISweden · Jul 10, 2023 · 1ec3a98 · 1ec3a98
1 parent 7adaa83
commit 1ec3a98
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Showing 164 changed files with 1,495 additions and 246 deletions.
diff --git a/bin/agat b/bin/agat
@@ -56,7 +56,7 @@ a GFF3 output by default. This can be tuned via the config file.
 
 Configuration (optional)
 ========================
-To access the config.yaml configuration file: agat config --expose
+To access the agat_config.yaml configuration file: agat config --expose
 The file will appear in the working folder. By default, AGAT uses the config file from the working directory when any.
 
 Feature levels (optional)
@@ -71,7 +71,7 @@ The file will appear in the working folder. By default, AGAT uses the config fil
          # 'config-files' => ["/etc/$APPNAME.json"],
          options     => [
             {
-               getopt      => 'help|h!',
+               getopt      => 'h|help!',
 					shortbool   => 1, #shortbool added by JDainat to avoid --no-help
                help        => 'Display the help',
             },
@@ -108,7 +108,7 @@ file. Indeed, if the feature_levels.yaml file exists in your working directory,
 used by default.',
          options     => [
 					 {
-							 getopt      => 'help|h!',
+							 getopt      => 'h|help!',
 							 shortbool   => 1,
 							 help        => 'Display the help',
 						},
@@ -136,15 +136,19 @@ force_gff_input_version, gtf_output_version, gff_output_version and output_forma
 ',
 				 options     => [
 					 {
-							getopt      => 'help|h!',
+							getopt      => 'h|help!',
 							help        => 'Display the help',
 							shortbool   => 1,
 					 },
 					 {
 							getopt      => 'expose|e!',
-							help        => 'Expose the config file (A config.yaml will be set in your working directory). If any AGAT use the config.yaml from the current directory over the default one.',
+							help        => 'Expose the config file. By default agat_config.yaml, but you can change the config file name using output option.',
 							shortbool   => 1,
 					 },
+					{
+							getopt      => 'output=s',
+							help        => 'To create a config file with the desired name instead of the default agat_config.yaml. Do not forget to mention your config file name when using AGAT, otherwise AGAT will use the agat_config.yaml in your working directory if any or the original agat_config.yaml file shiped along the tool.',
+					 },
 					 {
 							getopt      => 'verbose=i',
 							help        => 'Verbosity during the GFF/GTF parsing. 0 is quiet. 1,2,3 or 4 to increase verbosity.[Default 1]',

diff --git a/bin/agat_convert_bed2gff.pl b/bin/agat_convert_bed2gff.pl
@@ -8,7 +8,7 @@
 use AGAT::AGAT;
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $outfile = undef;
 my $bed = undef;
 my $source_tag = "data";
@@ -18,14 +18,16 @@
 my $verbose = undef;
 my $help;
 
-if( !GetOptions(  "help" => \$help,
-							    "bed=s" => \$bed,
-									"source=s" => \$source_tag,
-									"verbose|v!" => \$verbose,
-									"primary_tag=s" => \$primary_tag,
-									"inflate_off!" => \$inflating_off,
-									"inflate_type=s" => \$inflate_type,
-							    "outfile|output|o|out|gff=s" => \$outfile ) )
+
+if( !GetOptions(  	'c|config=s'     => \$config,
+					"h|help"         => \$help,
+					"bed=s"          => \$bed,
+					"source=s"       => \$source_tag,
+					"verbose|v!"     => \$verbose,
+					"primary_tag=s"  => \$primary_tag,
+					"inflate_off!"   => \$inflating_off,
+					"inflate_type=s" => \$inflate_type,
+					"outfile|output|o|out|gff=s" => \$outfile ) )
 {
     pod2usage( { -message => "Failed to parse command line.\n",
                  -verbose => 1,
@@ -46,6 +48,9 @@
            -exitval => 1 } );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+
 ## Manage output file
 my $gffout = prepare_gffout($config, $outfile);
 
@@ -487,6 +492,12 @@ =head1 OPTIONS
 Output GFF file. If no output file is specified, the output will be
 written to STDOUT.
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

diff --git a/bin/agat_convert_embl2gff.pl b/bin/agat_convert_embl2gff.pl
@@ -10,18 +10,18 @@
 use AGAT::AGAT;
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $outfile;
 my $embl;
 my $emblmygff3;
-my $throw_fasta=$config->{"throw_fasta"};
 my $primaryTags;
 my $discard;
 my $keep;
 my $help;
 
 if( !GetOptions(
-    "help"                       => \$help,
+    'c|config=s'                 => \$config,
+    "h|help"                     => \$help,
     "embl=s"                     => \$embl,
     "primary_tag|pt|t=s"         => \$primaryTags,
     "d!"                         => \$discard,
@@ -48,6 +48,10 @@
            -exitval => 1 } );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+my $throw_fasta=$config->{"throw_fasta"};
+
 ##################
 # MANAGE OPTION  #
 if($discard and $keep){
@@ -256,6 +260,12 @@ =head1 OPTIONS
 Output GFF file. If no output file is specified, the output will be
 written to STDOUT.
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

diff --git a/bin/agat_convert_genscan2gff.pl b/bin/agat_convert_genscan2gff.pl
@@ -9,7 +9,7 @@
 use AGAT::AGAT;
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $outfile = undef;
 my $genscan = undef;
 my $seq_id = "unknown";
@@ -19,11 +19,13 @@
 my $verbose = undef;
 my $help;
 
-if( !GetOptions(  "help" => \$help,
-							    "g|genscan=s" => \$genscan,
-								"seqid=s" => \$seq_id,
-								"verbose|v!" => \$verbose,
-							    "outfile|output|o|out|gff=s" => \$outfile ) )
+
+if( !GetOptions(    'c|config=s'                => \$config,
+					"h|help"                    => \$help,
+					"g|genscan=s"               => \$genscan,
+					"seqid=s"                   => \$seq_id,
+					"verbose|v!"                => \$verbose,
+					"outfile|output|o|out|gff=s" => \$outfile ) )
 {
     pod2usage( { -message => "Failed to parse command line.\n",
                  -verbose => 1,
@@ -44,6 +46,9 @@
            -exitval => 1 } );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+
 ## Manage output file
 my $gffout = prepare_gffout($config, $outfile);
 
@@ -301,6 +306,12 @@ =head1 OPTIONS
 Output GFF file. If no output file is specified, the output will be
 written to STDOUT.
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

diff --git a/bin/agat_convert_mfannot2gff.pl b/bin/agat_convert_mfannot2gff.pl
@@ -11,7 +11,7 @@
 use AGAT::AGAT;
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $mfannot_file;
 my $verbose;
 my $gff_file;
@@ -25,14 +25,18 @@
     'mfannot|m|i=s' => \$mfannot_file,
     'gff|g|o=s' => \$gff_file,
 		'v|verbose!' => \$verbose,
-    'help|h' => sub { pod2usage( -exitstatus=>0, -verbose=>99, -message => "$header\n" ); },
+    'c|config=s'               => \$config,
+    'h|help' => sub { pod2usage( -exitstatus=>0, -verbose=>99, -message => "$header\n" ); },
     'man' => sub { pod2usage(-exitstatus=>0, -verbose=>2); }
 ) or pod2usage ( -exitstatus=>2, -verbose=>2 );
 
 if (!defined $mfannot_file) {
     pod2usage( -message=>"Insufficient options supplied", -exitstatus=>2 );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+
 ## Manage output file
 my $gffout = prepare_gffout($config, $gff_file);
 
@@ -456,6 +460,12 @@ =head1 OPTIONS
 
 the gff output file
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

diff --git a/bin/agat_convert_minimap2_bam2gff.pl b/bin/agat_convert_minimap2_bam2gff.pl
@@ -9,7 +9,7 @@
 
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $opt_in;
 my $opt_bam;
 my $opt_sam;
@@ -20,6 +20,7 @@
                   'b|bam!' => \$opt_bam,
                   's|sam!' => \$opt_sam,
                   'o|out|output=s' => \$opt_output,
+                  'c|config=s'               => \$config,
                   'h|help!'         => \$opt_help ) )
 {
     pod2usage( { -message => 'Failed to parse command line',
@@ -41,6 +42,9 @@
            -exitval => 1 } );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+
 # ---- set output -----
 my $out_stream = prepare_gffout($config, $opt_output);
 
@@ -377,6 +381,12 @@ =head1 OPTIONS
 Output GFF file.  If no output file is specified, the output will be
 written to STDOUT.
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

diff --git a/bin/agat_convert_sp_gff2bed.pl b/bin/agat_convert_sp_gff2bed.pl
@@ -7,15 +7,16 @@
 use AGAT::AGAT;
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $outfile = undef;
 my $gff = undef;
 my $sub = "exon";
 my $opt_nc = "keep";
 my $help;
 
 if( !GetOptions(
-    "help|h" => \$help,
+    'c|config=s'               => \$config,
+    "h|help" => \$help,
     "gff=s" => \$gff,
     "sub=s" => \$sub,
     "nc=s" => \$opt_nc,
@@ -39,6 +40,9 @@
            -exitval => 1 } );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+
 ## Manage output file
 my $bedout;
 if ($outfile) {
@@ -258,6 +262,12 @@ =head1 OPTIONS
 
 File where will be written the result. If no output file is specified, the output will be written to STDOUT.
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

diff --git a/bin/agat_convert_sp_gff2gtf.pl b/bin/agat_convert_sp_gff2gtf.pl
@@ -7,7 +7,7 @@
 use AGAT::AGAT;
 
 my $header = get_agat_header();
-my $config = get_agat_config();
+my $config;
 my $outfile = undef;
 my $gff = undef;
 my $relax  = undef;
@@ -17,7 +17,8 @@
 
 
 if( !GetOptions(
-    "help" => \$help,
+    'c|config=s'               => \$config,
+    "h|help" => \$help,
     "gff|gtf|i=s" => \$gff,
 	"gtf_version=s" => \$gtf_version,
 	"verbose|v!" => \$verbose,
@@ -42,6 +43,9 @@
            -exitval => 1 } );
 }
 
+# --- Manage config ---
+$config = get_agat_config({config_file_in => $config});
+
 ## Manage output file
 my $gtf_out;
 if ($outfile) {
@@ -134,6 +138,12 @@ =head1 OPTIONS
 Output GTF file. If no output file is specified, the output will be
 written to STDOUT.
 
+=item B<-c> or B<--config>
+
+String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
+otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
+The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
+
 =item B<-h> or B<--help>
 
 Display this helpful text.