fix #401 (#466)

* Fix #401 by add yaml possible output for statistics script.
NBISweden · Jun 6, 2024 · 3b94442 · 3b94442
1 parent 0278734
commit 3b94442
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Showing 4 changed files with 188 additions and 97 deletions.
diff --git a/bin/agat_sp_statistics.pl b/bin/agat_sp_statistics.pl
@@ -13,6 +13,7 @@
 my $config;
 my $gff = undef;
 my $opt_output = undef;
+my $opt_yaml = undef;
 my $opt_genomeSize = undef;
 my $opt_plot = undef;
 my $opt_verbose = 0;
@@ -22,6 +23,7 @@
     'c|config=s'               => \$config,
     "h|help"      => \$opt_help,
     'o|output=s'  => \$opt_output,
+    'yaml!'       => \$opt_yaml,
     'd|p'         => \$opt_plot,
     'v|verbose'   => \$opt_verbose,
     'g|f|gs=s'    => \$opt_genomeSize,
@@ -52,6 +54,13 @@
 
 #### IN / OUT
 my $out = prepare_fileout($opt_output);
+if(defined($opt_yaml)){
+  if( defined($opt_output)){
+    $opt_yaml = $opt_output.".yaml";
+  }else{
+    $out
+  }
+}
 
 #Manage plot folder output
 if($opt_plot){
@@ -93,10 +102,11 @@
 ##############
 # STATISTICS #
 print "Compute statistics\n";
-print_omniscient_statistics ({ input => $hash_omniscient,
-															 genome => $opt_genomeSize,
-															 output => $out,
-															 distri => $opt_plot,
+print_omniscient_statistics ({ input   => $hash_omniscient,
+															 genome  => $opt_genomeSize,
+															 output  => $out,
+                               yaml    => $opt_yaml,
+															 distri  => $opt_plot,
 															 isoform => 1,
 															 verbose => $opt_verbose
 														 });
@@ -149,6 +159,10 @@ =head1 OPTIONS
 
 File where will be written the result. If no output file is specified, the output will be written to STDOUT.
 
+=item B<--yaml>
+
+Bolean - When this option is activated , a second output will be printed either in STDOUT if no output provided or in <output.yaml> (a .yaml suffix is added to the --output value provided)
+
 =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, 

diff --git a/docs/tools/agat_sp_statistics.md b/docs/tools/agat_sp_statistics.md
@@ -39,6 +39,10 @@ agat_sp_statistics.pl --help
 
     File where will be written the result. If no output file is specified, the output will be written to STDOUT.
 
+- **--yaml**
+
+    Bolean - When this option is activated , a second output will be printed either in STDOUT if no output provided or in <output.yaml> (a .yaml suffix is added to the --output value provided)
+
 - **-c** or **--config**
 
     String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any,