Bio-Procedural

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examples/bioperl.pl  view on Meta::CPAN

                  waitenter
                  # now the sequences are output in
                  # fasta format
                  # to change to embl format:
                  ^+outformat embl
                  ^,
                  waitenter
                  # we can also fetch _all_ seqs from
                  # a file; for this example we will
                  # use t/data/swiss.dat, which is in
                  # swiss format. usually bioperl can guess
                  # the file format from the file extension
                  # but this isn't possible here, so we
                  # must help by setting the input format:
                  ^+format swiss
                  # now lets get all the sequences, like this:
                  ^<*t/data/swiss.dat
                  waitenter
                  # typing <* is equivalent to
                  # using the read_seqs() function,
                  # like this:

lib/Bio/Perl.pm  view on Meta::CPAN

Bio::Perl - Functional access to BioPerl for people who don't know objects

=head1 VERSION

version 1.7.4

=head1 SYNOPSIS

  use Bio::Perl;

  # will guess file format from extension
  $seq_object = read_sequence($filename);

  # forces genbank format
  $seq_object = read_sequence($filename,'genbank');

  # reads an array of sequences
  @seq_object_array = read_all_sequences($filename,'fasta');

  # sequences are Bio::Seq objects, so the following methods work
  # for more info see Bio::Seq, or do 'perldoc Bio/Seq.pm'

lib/Bio/Perl.pm  view on Meta::CPAN

=head2 read_sequence

 Title   : read_sequence
 Usage   : $seq = read_sequence('sequences.fa')
           $seq = read_sequence($filename,'genbank');

           # pipes are fine
           $seq = read_sequence("my_fetching_program $id |",'fasta');

 Function: Reads the top sequence from the file. If no format is given, it will
           try to guess the format from the filename. If a format is given, it
           forces that format. The filename can be any valid perl open() string
           - in particular, you can put in pipes

 Returns : A Bio::Seq object. A quick synopsis:
           $seq_object->display_id - name of the sequence
           $seq_object->seq        - sequence as a string

 Args    : Two strings, first the filename - any Perl open() string is ok
           Second string is the format, which is optional

t/Perl.t  view on Meta::CPAN

    test_begin(-tests => 31,
               -requires_module => 'IO::String');

    use_ok('Bio::Perl');
}

# Bio::Perl isn't OO so we don't see Bio::Perl->new() here

my ($seq_object,$filename,$blast_report,@seq_object_array);

# will guess file format from extension
$filename = test_input_file('cysprot1.fa');
ok ($seq_object = read_sequence($filename));
isa_ok $seq_object, 'Bio::SeqI';

# forces genbank format
$filename = test_input_file('AF165282.gb');
ok  ($seq_object = read_sequence($filename,'genbank'));
isa_ok $seq_object, 'Bio::SeqI';

# reads an array of sequences