[Bioperl-l] All roads lead to Bio::Seq

[Ewan Birney]

I will soon commit this which is reorganise the documentation in
Bio::Seq, Bio::SeqI, Bio::PrimarySeqI and Bio::PrimarySeq to stress
that Bio::Seq has the best documentation and starting point for users
of the package. I am also using [Developers] in the =head1 NAME line to
indicate that a package is for developers only.

I will commit this because I think this is much much better than what is
there at the moment, which was pretty confusing, but recent-newbies - any
other thoughts about this synopsis and also any other reassuring words
to make in Bio::Seq?


Here is the Bio::Seq synopsis...



    # This is the main sequence object in Bioperl

    # gets a sequence from a file
    $seqio  = Bio::SeqIO->new( '-format' => 'embl' , -file => 'myfile.dat');
    $seqobj = $seqio->next_seq();

    # SeqIO can both read and write sequences; see Bio::SeqIO
    # for more information and examples

    # get from database
    $db = Bio::DB::GenBank->new();
    $seqobj = $db->get_Seq_by_acc('X78121');

    # make from strings in script
    $seqobj = Bio::Seq->new( -display_id => 'my_id',
			     -seq => $sequence_as_string);

    # gets sequence as a string from sequence object
    $seqstr   = $seqobj->seq(); # actual sequence as a string
    $seqstr   = $seqobj->subseq(10,50); # slice in biological coordinates

    # retrieves information from the sequence
    # features must implement Bio::SeqFeatureI interface

    @features = $seqobj->get_SeqFeatures(); # just top level
    foreach my $feat ( @features ) {
	print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
	$feat->end," strand ",$feat->strand,"\n";

        # features retain link to underlying sequence object
        print "Feature sequence is ",$feat->seq->seq(),"\n"
    }

    # sequences may have a species

    if( defined $seq->species ) {
	print "Sequence is from ",$species->binomial_name," [",$species->common_name,"]\n";
    }

    # annotation objects are Bio::AnnotationCollectionI's
    $ann      = $seqobj->annotation(); # annotation object

    # references is one type of annotations to get. Also get
    # comment and dblink. Look at Bio::AnnotationCollection for
    # more information

    foreach my $ref ( $ann->get_Annotations('reference') ) {
	print "Reference ",$ref->title,"\n";
    }

    # you can get truncations, translations and reverse complements, these
    # all give back Bio::Seq objects themselves, though currently with no
    # features transfered

    my $trunc = $seqobj->trunc(100,200);
    my $rev   = $seqobj->revcom();

    # there are many options to translate
    my $trans = $seqobj->translate();

    # these functions can be chained together

    my $trans_trunc_rev = $seqobj->trunc(100,200)->revcom->translate();