maintenance/ncbi_blast_switches.pl

   1 #!/usr/bin/perl
   2
   3 # This script determines all the valid command line switches
   4 # from the four main NCBI BLAST tools, and produces Perl code
   5 # to put into Bio/Tools/Run/StandAloneBlast.pm
   6 #
   7 # Torsten Seemann
   8 # 27 June 2006
   9
  10
  11 my @exe = qw(blastall blastpgp rpsblast bl2seq);
  12
  13 for my $exe (@exe) {
  14   open(HELP, "$exe - |") or die $!;
  15   my @switch;
  16   while (<HELP>) {
  17     next unless m/^\s*-(\w)\s/;
  18     push @switch, $1;
  19   }
  20   close(HELP);
  21   print "\t\@",uc($exe),"_PARAMS = qw(", join(q{ }, sort @switch), ");\n";
  22 }
  23