From Code to Community: Sponsoring The Perl and Raku Conference 2025 Learn more

SENDU / bioperl-1.5.2_004-RCd / t / GuessSeqFormat.t 

            

              
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133

              
# -*-Perl-*- mode (to keep my emacs happy)
# $Id: GuessSeqFormat.t,v 1.8 2005/01/12 17:15:21 jason Exp $
# test for Bio::Tools::GuessSeqFormat
# written by Heikki Lehvaslaiho
use strict;
my $NUMTESTS;
my $error;
BEGIN {
   eval { require Test; };
   if( $@ ) {
      use lib 't','..';
   }
   use Test;
   $error = 0;
   # SeqIO::game needs XML::Writer
   eval {require XML::Writer};
   if ($@) {
      print STDERR "XML::Writer not found, skipping game test\n";
      $error = 1;
   }
   $NUMTESTS = ($error == 1) ? 44 : 46;
   plan tests => $NUMTESTS;
}
my @seqformats = qw{ ace embl fasta gcg genbank mase
                        pfam pir raw swiss tab };
push @seqformats,"game" if ($error == 0);
use Bio::SeqIO;
use Bio::AlignIO;
use Bio::Tools::GuessSeqFormat;
use Data::Dumper;
ok 1;
my $format;
my $verbose =1;
#
# Seqio formats
#
#not tested:  waba
my %no_seqio_module = map {$_=>1} qw {gcgblast gcgfasta mase pfam};
my $guessed_format = new Bio::Tools::GuessSeqFormat
        (-file => Bio::Root::IO->catfile("t","data","test.waba"))->guess;
ok $guessed_format, undef ;
eval {
    my $input = Bio::SeqIO->new
        (-file=>Bio::Root::IO->catfile("t","data","test.waba"));
    ok my $seq = $input->next_seq();
};
$@ ? ok 1 : ok 0;
foreach $format (@seqformats) {
    my $guessed_format = new Bio::Tools::GuessSeqFormat
        (-file => Bio::Root::IO->catfile("t","data","test.$format"),
         #-verbose=> $verbose;
        )->guess;
    $format =~ s/\..*$//;
    ok $guessed_format, $format;
    next if $no_seqio_module{$format};
    eval {
        my $input = Bio::SeqIO->new
            (-file=>Bio::Root::IO->catfile("t","data","test.$format"));
        ok my $seq = $input->next_seq();
    };
    ok 0, 1, $@ if $@;
}
#
# AlignIO formats
#
@seqformats = qw{ aln:clustalw fasta mase msf nexus pfam phylip
                  prodom stockholm}; # not selex (same as pfam, mainly)
my %no_alignio_module = map {$_=>1} qw {};
foreach my $ext (@seqformats) {
    my $format;
    ($ext, $format) = split /:/, $ext;
    my $guesser = new Bio::Tools::GuessSeqFormat
        (-file => Bio::Root::IO->catfile("t","data","testaln.$ext"));
    $format ||= $ext;
    ok $guesser->guess(), $format;
    next if $no_alignio_module{$format};
    eval {
        my $input = Bio::AlignIO->new
            (-file=>Bio::Root::IO->catfile("t","data","testaln.$ext"));
        ok my $seq = $input->next_aln();
    };
    ok 0, 1, $@ if $@;
}
#
# File handle tests
#
if( eval 'require IO::String; 1' ) {
    my $string = ">test1 no comment
agtgctagctagctagctagct
>test2 no comment
gtagttatgc
";
    my $stringfh = new IO::String($string);
     
    my $seqio = new Bio::SeqIO(-fh => $stringfh);
    while( my $seq = $seqio->next_seq ) {
        ok $seq->id =~ /test/;
    }
     
#
# text guessing
#
    ok new Bio::Tools::GuessSeqFormat( -text => $string )->guess, 'fasta';
} else {
    for (1..3) {
        skip("skipping guessing format from string, IO::String not installed",1);
    }
}