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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 105);
use_ok 'Bio::Tools::GuessSeqFormat';
use_ok 'Bio::SeqIO';
use_ok 'Bio::AlignIO';
}
ok my $guesser = Bio::Tools::GuessSeqFormat->new;
isa_ok $guesser, 'Bio::Tools::GuessSeqFormat';
#
# Test guesser interfaces
#
# 1/ File guess
ok $guesser = Bio::Tools::GuessSeqFormat->new(
-file => test_input_file('test.fasta'),
), 'File input';
is $guesser->guess, 'fasta';
# 2/ String guess
my $string = ">test1 no comment
agtgctagctagctagctagct
>test2 no comment
gtagttatgc
";
ok $guesser = Bio::Tools::GuessSeqFormat->new(
-text => $string,
), 'String input';
is $guesser->guess, 'fasta';
# 3/ Filehandle guess
SKIP: {
test_skip(-tests => 2, -requires_modules => [qw(IO::String)]);
require IO::String;
my $fh = IO::String->new($string);
ok $guesser = Bio::Tools::GuessSeqFormat->new(
-fh => $fh,
), 'Filehandle input';
is $guesser->guess, 'fasta';
}
#
# Test behavior with unknown format
#
is $guesser = Bio::Tools::GuessSeqFormat->new(
-file => test_input_file('test.waba'), # Bio::SearchIO::waba
)->guess, undef, 'Unknown file format';
throws_ok {
Bio::SeqIO->new( -file=>test_input_file('test.waba') );
} qr/Could not guess format/;
#
# Test SeqIO formats
#
my @fmts = qw{ace embl fasta fastq game gcg genbank pir raw swiss tab};
for my $fmt (@fmts) {
SKIP: {
test_skip(
-tests => 4,
-requires_modules => [qw(XML::Writer XML::Parser::PerlSAX)]
) if $fmt eq 'game';
test_skip(
-tests => 4,
-requires_module => 'Data::Stag'
) if $fmt eq 'swiss';
my $guess = Bio::Tools::GuessSeqFormat->new(
-file => test_input_file("test.$fmt"),
)->guess;
is $guess, $fmt, "$fmt format";
ok my $input = Bio::SeqIO->new( -file=>test_input_file("test.$fmt") );
ok my $seq = $input->next_seq();
isa_ok $seq, 'Bio::PrimarySeqI';
}
}
#
# Test AlignIO formats
#
@fmts = qw{clustalw fasta fastq mase mega msf nexus pfam phylip prodom selex};
## Instead of this, we should instead have a mock of those modules.
## Two reasons: 1) this modules are dependent on ourselves so this
## tests will only be triggered when updating. 2) it's not really our
## job to check if the other module reads file correctly, we just need
## to ensure that it's called to read the file.
SKIP: {
test_skip(-tests => 4,
-requires_modules => ['Bio::AlignIO::stockholm']);
push(@fmts, 'stockholm');
}
my %skip_module = map {$_=>1} qw{ fastq };
for my $fmt (@fmts) {
my $guess = Bio::Tools::GuessSeqFormat->new(
-file => test_input_file("testaln.$fmt")
)->guess;
is $guess, $fmt, "$fmt format";
next if $skip_module{$fmt};
ok my $input = Bio::AlignIO->new( -file=>test_input_file("testaln.$fmt") );
ok my $seq = $input->next_aln();
isa_ok $seq, 'Bio::Align::AlignI';
}
#
# Other formats
#
my %fmts = (
blast => test_input_file('blastp2215.blast'),
gcgblast => test_input_file('test.gcgblast'),
vcf => test_input_file('example.vcf'),
);
while (my ($fmt, $file) = each %fmts) {
my $guess = Bio::Tools::GuessSeqFormat->new(
-file => $file,
)->guess;
is $guess, $fmt, "$fmt format";
}
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