t/legacy/integration/tools/sigpep_find.t

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4 use English;
   5
   6 use Test::More tests => 11;
   7
   8 use lib 't/lib';
   9 use SGN::Test::WWW::Mechanize;
  10
  11 my @invalid_seqs =
  12     ( [ 'SGN-U409494-translated',
  13         'MGRMNGNPSARKSKGGEYLYDLCFLPFDSADQIGGIILYCCVGLSSFLASSLSASSSSRMSFENAPGFAFIQFCRATKGWTQSEPXKRVD
  14 TIRALFFCRAFEETEESTRELSTTGAVPQMSNARAVQGFLSLPSRDSFSSSAPYAAASAIKESREGCGEGDWGVGAVAVAAAVDEFDPPR
  15 RHLPSRSGSALDP*'
  16       ],
  17       [ 'SGN-U442055-translated',
  18         'TPHAAAEDILFFAQHSAGTENAAVIKQRLGSLRKKSGHETANXAAVKIIVAIIPNLXAAWAYYQVNDLLQFQSKRWLSKLNFVRDKQNVF
  19 LHWIMQRKVNHLSLLIVNLMGNDHGCVIFISVLAFEVVYASLNPVMTNYSEIELDEPIRRPNIVDEAAKTAASQHLTPPISDRKSWGQPK
  20 YFTCWSIENSLSTDTVGVRFAYYLSFPHPX ',
  21       ],
  22     );
  23
  24 my @no_hits_seqs =
  25     (['SGN-U569791','VIRQFILSVLRTYTFFSFSLSECGQIMSLKNRERPTESIILNKETEGSCINTSENSSEI'],
  26     );
  27
  28 my $input_page = "/tools/sigpep_finder/input.pl";
  29
  30 my $mech = SGN::Test::WWW::Mechanize->new;
  31
  32 # single sequence submission, no ending newline
  33 {
  34     $mech->get_ok( $input_page );
  35
  36     # a few checks on the title
  37     $mech->title_like( qr/Signal peptide finder/i, "Make sure we're on sigpep input page" );
  38
  39     # a few checks on the content
  40     $mech->content_contains( "HMMER", "mentions HMMER" );
  41
  42     $mech->submit_form_ok({ form_name => 'sigseq_form',
  43                             fields =>
  44                             {
  45                              sequences => ">$invalid_seqs[0]->[0]\n$invalid_seqs[0]->[1]",
  46                              display_opt => 'filter',
  47 #                              use_eval_cutoff => 1,
  48 #                                eval_cutoff => 2,
  49 #                              use_bval_cutoff => 1,
  50 #                                bval_cutoff => 0,
  51                             },
  52                           },
  53                           'submit a single sequence',
  54                          );
  55
  56     $mech->content_like( qr/illegal character/i, "mentions illegal characters" );
  57     $mech->content_like( qr/re-enter input/i, "says to re-enter input" );
  58
  59
  60     #submit a valid sequence
  61     $mech->get_ok( $input_page );
  62     $mech->submit_form_ok({ form_name => 'sigseq_form',
  63                             fields =>
  64                             {
  65                              sequences => ">$no_hits_seqs[0]->[0]\n$no_hits_seqs[0]->[1]\n\n",
  66                              display_opt => 'filter',
  67 #                              use_eval_cutoff => 1,
  68 #                                eval_cutoff => 2,
  69 #                              use_bval_cutoff => 1,
  70 #                                bval_cutoff => 0,
  71                             },
  72                           },
  73                           'submit a single sequence',
  74                          );
  75
  76     $mech->content_like( qr/no hits/i, "mentions no hits" );
  77     $mech->content_like( qr/Results/i, "mentions results" );
  78     $mech->content_like( qr/histogram/i, "mentions histogram" );
  79 }
  80
  81
  82