polish parameter call

NBISweden · May 20, 2020 · 804d9e8 · 804d9e8
1 parent f212f5f
commit 804d9e8
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Showing 2 changed files with 16 additions and 10 deletions.
diff --git a/annotation/tools/fasta/gaas_fasta_splitter.pl b/annotation/tools/fasta/gaas_fasta_splitter.pl
@@ -13,7 +13,7 @@
 my $start_run = time();
 
 my $opt_fastafile;
-my $opt_output;
+my $opt_output="split_result";
 my $opt_help = undef;
 my $opt_nb_chunk;
 my $opt_leftover="attach";
@@ -48,10 +48,10 @@
 }
 
 # ---- check options ----
-if (! ( $opt_fastafile or $opt_output ) ) {
+if (! ( $opt_fastafile and ($opt_nb_chunk or $opt_nb_seq_by_chunk)) ) {
  pod2usage( {
  -message => "\nAt least 2 parameters are mandatory:\nInput reference fasta file (-f)".
- "Output folder (-o)\n\n".
+ "\nnumber of chuncks (--nb_chunks) or/and number of sequences by chunk (--nb_seq_by_chunk)\n\n".
  "Look at the help documentation to know more.\n",
  -verbose => 0,
  -exitval => 2 } );
@@ -92,6 +92,10 @@
  print "=> <leftover> option is $opt_leftover\n";
  }
 }
+
+if(! -f $opt_fastafile){
+ print "$opt_fastafile is not a file\n."; exit;
+}
 # ----- output -------
 
 my ($inputname,$path,$ext) = fileparse($opt_fastafile,qr/\.[^.]*/);
@@ -460,8 +464,7 @@ =head1 OPTIONS
 
 =item B<-o> or B<--output>
 
-Output fasta file. If no output file is specified, the output will be
-written to STDOUT.
+Output folder. Default split_result
 
 =item B<-h> or B<--help>
 

diff --git a/bin/gaas_fasta_splitter.pl b/bin/gaas_fasta_splitter.pl
@@ -13,7 +13,7 @@
 my $start_run = time();
 
 my $opt_fastafile;
-my $opt_output;
+my $opt_output="split_result";
 my $opt_help = undef;
 my $opt_nb_chunk;
 my $opt_leftover="attach";
@@ -48,10 +48,10 @@
 }
 
 # ---- check options ----
-if (! ( $opt_fastafile or $opt_output ) ) {
+if (! ( $opt_fastafile and ($opt_nb_chunk or $opt_nb_seq_by_chunk)) ) {
  pod2usage( {
  -message => "\nAt least 2 parameters are mandatory:\nInput reference fasta file (-f)".
- "Output folder (-o)\n\n".
+ "\nnumber of chuncks (--nb_chunks) or/and number of sequences by chunk (--nb_seq_by_chunk)\n\n".
  "Look at the help documentation to know more.\n",
  -verbose => 0,
  -exitval => 2 } );
@@ -92,6 +92,10 @@
  print "=> <leftover> option is $opt_leftover\n";
  }
 }
+
+if(! -f $opt_fastafile){
+ print "$opt_fastafile is not a file\n."; exit;
+}
 # ----- output -------
 
 my ($inputname,$path,$ext) = fileparse($opt_fastafile,qr/\.[^.]*/);
@@ -460,8 +464,7 @@ =head1 OPTIONS
 
 =item B<-o> or B<--output>
 
-Output fasta file. If no output file is specified, the output will be
-written to STDOUT.
+Output folder. Default split_result
 
 =item B<-h> or B<--help>