view release on metacpan or  search on metacpan

t/50.synopsis.t  view on Meta::CPAN

  }
  
  # for retrieving up- and downstream regions,
  # Vmatch internal sequence ids are required
  # (no showdesc possible)

  $sbe->search({
    query   => 'AGAGCCCT',
    reverse_complement => 1,
    mismatches         => 1,
    upstream           => 30,
    downstream         => 30,
  });
 
  my @internal_ids;
  while ( my $res = $sbe->next_res ) {
    # vsubseqselect is called now for every result ...
    push @internal_ids, $res->sequence_id;
  }

  # ... but one can retrieve all complete sequences with
  # just one call of vseqselect
  my $seq_io = $sbe->get_sequences(\@internal_ids);

EOT
;
    eval $code;
    ok(!code_eval($code),"Vmatch SYNOPSIS compiles") || diag $@;


$code =<<'EOT'
  use Bio::Grep;
  use Bio::SeqIO;
 
  my $sbe = Bio::Grep->new('Vmatch');
 
  my $out = Bio::SeqIO->new( -format => 'Fasta',
                             -file   => '>motifs.fasta',
                           );
 
  # you have an array with DNA sequences
  my @motifs = ( 'aaaaaa', 'gggggg' );
  
  for my $i (0 .. $#motifs ) {
     my $seq = Bio::Seq->new(
             -id => $i,
             -seq => $motifs[$i],
         );
     $out->write_seq($seq);
  }
 
  $sbe->search({
     datapath   => 't/data',
     database   => 'ATH1.cdna',
     query_file => 'motifs.fasta',
     complete   => 1,
  });

EOT
;
    ok(!code_eval($code),"Cookbook recipe motifs solution a compiles") || diag $@;

    unlink 'motifs.fasta';
}

# Agrep
$backendname  = 'Agrep';

SKIP:{

    skip 'Agrep binary not in path', 1 if
        BioGrepSkip::find_binary_in_path( lc($backendname) ) eq '';

    delete_files;
    mkdir 't/data';

my $code =<<'EOT'
  use Bio::Grep;
  
  my $sbe = Bio::Grep->new('Agrep');
  
  # generate a database. you have to do this only once. 
  $sbe->generate_database({ 
    file        => 't/Test_DB_RevCom.fasta', 
    description => 'AGI Transcripts',
    datapath    => 'data',
  });
  
  # search for the reverse complement and allow 2 mismatches 
  # Don't calculate Alignments with EMBOSS
  $sbe->search({
    query   => 'GAGCCCTT',
    reverse_complement => 1, 
    mismatches         => 2,
    no_alignments      => 1,
    database           => 'ATH1.cdna',
  });
  
  my @internal_ids;
  
  # output the searchresults with nice alignments
  while ( my $res = $sbe->next_res) {
     print $res->sequence->id . "\n";
     # print $res->alignment_string() . "\n\n";
     push @internal_ids, $res->sequence_id;
  }
  
  # get the complete sequences as Bio::SeqIO object
  my $seq_io = $sbe->get_sequences(\@internal_ids);


EOT
;
    ok(!code_eval($code),"Agrep SYNOPSIS compiles") || diag $@;
}
    

# GUUGle
$backendname  = 'GUUGle';

SKIP:{

t/50.synopsis.t  view on Meta::CPAN

  my $sbe = Bio::Grep->new('RE');
  
  $sbe->settings->datapath('data');
  
  # generate a database. you have to do this only once. 
  $sbe->generate_database({ 
    file        => 't/Test_DB_RevCom.fasta', 
    description => 'AGI Transcripts',
    datapath    => 'data',
  });
  
  # search on both strands  
  # retrieve up- and downstream regions of size 30
  
  $sbe->search({
    query   => 'GAGCCCTT',
    direct_and_rev_com => 1, 
    upstream           => 30,
    downstream         => 30,
    database           => 'ATH1.cdna',
  });
  
  my @internal_ids;
  
  # output the searchresults with nice alignments
  while ( my $res = $sbe->next_res) {
     print $res->sequence->id . "\n";
     print $res->mark_subject_uppercase() . "\n";
     print $res->alignment_string() . "\n\n";
     push @internal_ids, $res->sequence_id;
  }
  
  # get the complete sequences as Bio::SeqIO object
  my $seq_io = $sbe->get_sequences(\@internal_ids);

  # sequences with at least 10 As
  $sbe->search({ query => '[A]{10,}' });
 
  # some SNPs
  $sbe->search({query => '[CG]TGC[AT]CTCTTCT[CG]TCA'});

EOT
;
ok(!code_eval($code),"RE SYNOPSIS compiles") || diag $@;

$code =<<'EOT'
  use Bio::Grep;
 
  my $sbe = Bio::Grep->new('RE');
 
  my $motif = '[AC]{4}TAAAA[AGCT]GG';
 
  $sbe->search({
     datapath  => 't/data',
     database  => 'Test_DB_RevCom.fasta',
     query      => $motif,
  });
EOT
;
eval $code;
ok(!$@,"Cookbook recipe motifs solution b compiles") || diag $@;

$code = 'bllll';
eval $code;
ok(code_eval($code),"bllll not compiles");

delete_files;
rmdir('t/tmp');
rmdir('t/data');
rmdir('t/data2');

sub code_eval {
    my ( $code ) = @_;
    $code =~ s/ATH1.cdna/Test_DB_RevCom.fasta/g;
    $code =~ s{'data'}{'t/data'}g;
    $code =~ s{generate_database\('T}{generate_database('t/T}g;
#    diag $code;
    eval $code;
    return $@;
}    
1;

# vim: ft=perl sw=4 ts=4 expandtab