t/SeqIO/raw.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests               => 25,
  10                            -requires_modules    => [],
  11                            -requires_networking => 0,
  12                           );
  13
  14         use_ok('Bio::SeqIO::raw');
  15 }
  16
  17 my $verbose = test_debug();
  18
  19 my $format = 'raw';
  20 my $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test.$format"),
  21                                                         -format => $format);
  22
  23 isa_ok($seqio_obj, 'Bio::SeqIO');
  24
  25
  26 is $seqio_obj->variant, 'multiple';
  27
  28 my @methods = qw(next_seq write_seq);
  29 foreach my $method (@methods) {
  30         can_ok($seqio_obj, $method) ||
  31                 diag "$method method not implemented for $format";
  32 }
  33
  34 # checking the first sequence object
  35 my $seq_obj = $seqio_obj->next_seq();
  36 isa_ok($seq_obj, 'Bio::Seq');
  37 my %expected = ('seq'         => 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGL' .
  38                                                                  'DYRTTDENLKAHEKWGNIVDVVVMKDPRTKRSRGFGFI' .
  39                                                                  'TYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPN' .
  40                                                                  'AGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDNIVI' .
  41                                                                  'DKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVD' .
  42                                                                  'VKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGN' .
  43                                                                  'QNGGGNWNNGGNNWGNNRGNDNWGNNSFGGGGGGGGGY' .
  44                                                                  'GGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGNDFGGY' .
  45                                                                  'QQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGN' .
  46                                                                  'YGNNQGFNNGGNNRRY',
  47                                 'length'      => '358',
  48                            );
  49 is   ($seq_obj->seq(),         $expected{'seq'},         'sequence');
  50 is   ($seq_obj->length(),      $expected{'length'},      'length');
  51
  52
  53 # checking the second sequence object
  54 my $seq_obj2  = $seqio_obj->next_seq();
  55 isa_ok($seq_obj2, 'Bio::Seq');
  56 my %expected2 = ('seq'         => 'MNKQRGTYSEVSLAQDPKRQQRKLKGNKISISGTKQEI' .
  57                                                                   'FQVELNLQNASSDHQGNDKTYHCKGLLPPPEKLTAEVL' .
  58                                                                   'GIICIVLMATVLKTIVLIPCIGVLEQNNFSLNRRMQKA' .
  59                                                                   'RHCGHCPEEWITYSNSCYYIGKERRTWEERVCWPVLRR' .
  60                                                                   'TLICFL',
  61                                  'length'      => '158',
  62                             );
  63 is   ($seq_obj2->seq(),         $expected2{'seq'},         'sequence');
  64 is   ($seq_obj2->length(),      $expected2{'length'},      'length');
  65
  66 # from testformats.pl
  67 SKIP: {
  68
  69     test_skip(-tests => 2,
  70               -requires_modules => [qw(Algorithm::Diff
  71                                     IO::ScalarArray
  72                                     IO::String)]);
  73     use_ok('Algorithm::Diff', qw(diff LCS));
  74
  75         my ($file, $type) = ("test.$format", $format);
  76     my $filename = test_input_file($file);
  77     print "processing file $filename\n" if $verbose;
  78     open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
  79     my @datain = <$FILE>;
  80     close $FILE;
  81
  82     my $in = IO::String->new(join('', @datain));
  83     my $seqin = Bio::SeqIO->new( -fh => $in,
  84                 -format => $type);
  85     my $out = IO::String->new;
  86     my $seqout = Bio::SeqIO->new( -fh => $out,
  87                  -format => $type);
  88     my $seq;
  89     while( defined($seq = $seqin->next_seq) ) {
  90         $seqout->write_seq($seq);
  91     }
  92     $seqout->close();
  93     $seqin->close();
  94     my $strref = $out->string_ref;
  95     my @dataout = map { $_."\n"} split(/\n/, $$strref );
  96     my @diffs = &diff( \@datain, \@dataout);
  97     is(@diffs, 0, "$format format can round-trip");
  98
  99     if(@diffs && $verbose) {
 100         use Data::Dumper;  # should be safe for 5.005 and greater
 101         foreach my $d ( @diffs ) {
 102             print STDERR Dumper $d;
 103             foreach my $diff ( @$d ) {
 104                 chomp($diff->[2]);
 105                 print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
 106             }
 107         }
 108         print "in is \n", join('', @datain), "\n";
 109         print "out is \n", join('',@dataout), "\n";
 110     }
 111 }
 112
 113 # test raw variants
 114 my @seq = qw(MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHEKWGNIVDVV
 115 VMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVEPKRAVPRQDIDSPNAGATVK
 116 KLFVGALKDDHDEQSIRDYFQHFGNIVDNIVIDKETGKKRGFAFVEFDDYDPVDKVVLQK
 117 QHQLNGKMVDVKKALPKNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGN
 118 NWGNNRGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNWNGGND
 119 FGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGNNQGFNNGGNNRRY);
 120
 121 $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test2.raw"),
 122                                                         -format => 'raw');
 123
 124 is($seqio_obj->variant, 'multiple');
 125
 126 my $ct = 0;
 127
 128 while (my $seq = $seqio_obj->next_seq) {
 129     is($seq->seq, $seq[$ct]);
 130     $ct++;
 131 }
 132
 133 is($ct, 6);
 134
 135 $seqio_obj = Bio::SeqIO->new(-file   => test_input_file("test2.raw"),
 136                                                         -format => 'raw-single');
 137
 138 is($seqio_obj->variant, 'single');
 139
 140 my $seq = $seqio_obj->next_seq;
 141 is($seq->seq, join('', @seq));
 142
 143 $seqio_obj = Bio::SeqIO->new(-file      => test_input_file("test2.raw"),
 144                             -format     => 'raw',
 145                             -variant    => 'single');
 146
 147 is($seqio_obj->variant, 'single');
 148
 149 $seq = $seqio_obj->next_seq;
 150 is($seq->seq, join('', @seq));