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t/24-bioperl-alignio.t  view on Meta::CPAN

$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
$str = Bio::AlignIO->new(
    '-file'    => test_input_file("UnaSmithHIV-both.nex"),
    '-format'  => 'nexus',
    '-verbose' => -1,
);
isa_ok( $str, 'Bio::AlignIO' );
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
$str = Bio::AlignIO->new(
    '-file'    => test_input_file("quoted-strings2.nex"),
    '-format'  => 'nexus',
    '-verbose' => -1,
);
isa_ok( $str, 'Bio::AlignIO' );
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
$str = Bio::AlignIO->new(
    '-file'    => test_input_file("barns-combined.nex"),
    '-format'  => 'nexus',
    '-verbose' => -1,
);
isa_ok( $str, 'Bio::AlignIO' );
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
$str = Bio::AlignIO->new(
    '-file'    => test_input_file("radical-whitespace.nex"),
    '-format'  => 'nexus',
    '-verbose' => -1,
);
isa_ok( $str, 'Bio::AlignIO' );
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
$str = Bio::AlignIO->new(
    '-file'    => test_input_file("basic-bush.nex"),
    '-format'  => 'nexus',
    '-verbose' => -1,
);
isa_ok( $str, 'Bio::AlignIO' );
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
$str = Bio::AlignIO->new(
    '-file'    => test_input_file("radical-whitespace_02.nex"),
    '-format'  => 'nexus',
    '-verbose' => -1,
);

# EMBOSS water
$str = Bio::AlignIO->new(
    '-format'  => 'emboss',
    '-file'    => test_input_file('cysprot.water'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->score,                      '501.50' );
is( $aln->get_seq_by_pos(1)->get_nse, 'PAPA_CARPA/3-342' );
is( $aln->get_seq_by_pos(2)->get_nse, 'CATL_HUMAN/1-331' );
SKIP: {
    skip 'percentage identity', 2, if 1;
    is( sprintf( "%.1f", $aln->overall_percentage_identity ), 33.8 );
    is( sprintf( "%.1f", $aln->average_percentage_identity ), 40.1 );
}
is( $aln->get_seq_by_pos(1)->start, 3 );
SKIP: {
    skip 'length', 1, if 1;
    is( $aln->length, 364 );
}

# EMBOSS needle
$str = Bio::AlignIO->new(
    '-format'  => 'emboss',
    '-file'    => test_input_file('cysprot.needle'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->score,                      '499.50' );
is( $aln->get_seq_by_pos(1)->get_nse, 'PAPA_CARPA/1-345' );
is( $aln->get_seq_by_pos(2)->get_nse, 'CATL_HUMAN/1-333' );

# EMBOSS water 2.2.x
$str = Bio::AlignIO->new(
    '-format'  => 'emboss',
    '-file'    => test_input_file('cys1_dicdi.water'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->get_seq_by_pos(1)->get_nse, 'CYS1_DICDI/1-343' );
is( $aln->get_seq_by_pos(2)->get_nse, 'CYS1_DICDI-1/1-343' );
is( $aln->score,                      '1841.0' );
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->get_seq_by_pos(1)->get_nse, 'CYS1_DICDI/29-343' );
is( $aln->get_seq_by_pos(2)->get_nse, 'ALEU_HORVU/61-360' );

# EMBOSS water 2.2.x sparse needle
$str = Bio::AlignIO->new(
    -verbose   => $DEBUG,
    '-format'  => 'emboss',
    '-file'    => test_input_file('sparsealn.needle'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->score, '18.0' );
is( sprintf( "%.1f", $aln->overall_percentage_identity ), 2.1 );
is( sprintf( "%.1f", $aln->average_percentage_identity ), 38.5 );
is( $aln->get_seq_by_pos(1)->length,  238 );
is( $aln->length,                     238 );
is( $aln->get_seq_by_pos(1)->get_nse, 'KV1K_HUMAN/1-108' );
is( $aln->get_seq_by_pos(2)->get_nse, 'IF1Y_HUMAN/1-143' );
is( $aln->get_seq_by_pos(1)->seq(),
        'DIQMTQSPSTLSVSVGDRVTITCEASQTVLSYLNWYQQK'
      . 'PGKAPKLLIYAASSLETGVPSRFSGQGSGTBFTFTISSVZPZBFATYYCQZYLDLPRTFGQGTKVDLKR'
      . '-' x 130 );
is( $aln->get_seq_by_pos(2)->seq(),
        ( '-' x 94 )
      . 'PKNKGKGGK-NRRRGKNENESEKRELVFKE'
      . 'DGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEAR'
      . 'SLKAYGGLPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI' );
is( $aln->is_flush, 1 );

# MEGA
$str = Bio::AlignIO->new(
    '-format'  => 'mega',
    '-file'    => test_input_file("hemoglobinA.meg"),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->get_seq_by_pos(1)->get_nse, 'Human/1-141' );
is( $aln->get_seq_by_pos(2)->get_nse, 'Horse/1-144' );
$aln->unmatch();
is( $aln->get_seq_by_pos(3)->subseq( 1, 10 ), 'V-LSAADKGN' );
$strout = Bio::AlignIO->new(
    '-format'  => 'mega',
    '-file'    => ">" . test_output_file(),
    '-verbose' => -1,
);
$status = $strout->write_aln($aln);
is $status, 1, "mega output test";

# EMBOSS needle
$str = Bio::AlignIO->new(
    '-format'  => 'emboss',
    '-file'    => test_input_file('gf-s71.needle'),
    '-verbose' => -1,
);
$aln = Bio::Phylo::Matrices::Matrix->new_from_bioperl( $str->next_aln() );
isa_ok( $aln, 'Bio::Align::AlignI' );
is( $aln->get_seq_by_pos(2)->seq(),
'MEDVTLFQFTWRKPI-RLQGEIVYKTSETQTIETNKKDVECVANFQENKEVQTDS-VDNGVGENVKKDITISKEVLNLLYDFVRDDSKVNYDRLLEFHKFDKVALETVQKYHVETRNENIILMISSSSRKTLILFGGISHETFCSHQARALLCSSSTSFSIPLPVCAISAVFYSSTQFILGDVSGNISMCSKDKIIFEKKITDGAVTCLEMCRHGLLSGSDDGNIILWQIGTSGLEKLGGTKLTVSDLS...
);
is( $aln->get_seq_by_pos(1)->seq(),
'MEDVTLHHFRWRKPVENKNGEIVYKTSETQTAEISRKDVECVANFQKSQESQTDDFMQNGVGDGIKKEIRISKEVLGHIYDFLRDDSKVNYDRLLEFHKFDKVSLETVQKYHVETRNENIILMISNSSRKTLILFGGLSHETFCSHQARAVLCSSSTTSSLPLPVCAISAVFYSSTQFLLGDISGNISMWTKEKMIFENKVTDGSVTSLELCRYGLLSGSDDGNVILWKVEESKIEKIEGIKLTVSDLS...
);
is( $aln->is_flush(),                 1 );
is( $aln->get_seq_by_pos(1)->get_nse, 'gf.s71.44/1-448' );
is( $aln->get_seq_by_pos(2)->get_nse, 'Y50C1A.2/1-406' );

# PHYLIP sequential/non-interleaved
$strout = Bio::AlignIO->new(
    '-file'    => test_input_file('noninterleaved.phy'),
    '-format'  => 'phylip',
    '-verbose' => -1,
);
$aln =