t/SeqIO/raw.t

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