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Bio::Seq::SeqBuilder.3pm

NAME

Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers

SYNOPSIS

    use Bio::SeqIO;
 
    # usually you won't instantiate this yourself - a SeqIO object -
    # you will have one already
    my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => "genbank");
    my $builder = $seqin->sequence_builder();
 
    # if you need only sequence, id, and description (e.g. for 
    # conversion to FASTA format):
    $builder->want_none();
    $builder->add_wanted_slot('display_id','desc','seq');
 
    # if you want everything except the sequence and features
    $builder->want_all(1); # this is the default if it's untouched
    $builder->add_unwanted_slot('seq','features');
 
    # if you want only human sequences shorter than 5kb and skip all
    # others
    $builder->add_object_condition(sub {
        my $h = shift;
        return 0 if $h->{'-length'} > 5000;
        return 0 if exists($h->{'-species'}) &&
                    ($h->{'-species'}->binomial() ne "Homo sapiens");
        return 1;
    });
 
    # when you are finished with configuring the builder, just use
    # the SeqIO API as you would normally
    while(my $seq = $seqin->next_seq()) {
        # do something
    }
 
 

DESCRIPTION

This is an implementation of Bio::Factory::ObjectBuilderI used by parsers of rich sequence streams. It provides for a relatively easy-to-use configurator of the parsing flow.

Configuring the parsing process may be for you if you need much less information, or much less sequence, than the stream actually contains. Configuration can in both cases speed up the parsing time considerably, because unwanted sections or the rest of unwanted sequences are skipped over by the parser. This configuration could also conserve memory if you're running out of available RAM.

See the methods of the class-specific implementation section for further documentation of what can be configured.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : my $obj = Bio::Seq::SeqBuilder->new();
  Function: Builds a new Bio::Seq::SeqBuilder object 
  Returns : an instance of Bio::Seq::SeqBuilder
  Args    :
 
 

Methods for implementing Bio::Factory::ObjectBuilderI

want_slot

  Title   : want_slot
  Usage   :
  Function: Whether or not the object builder wants to populate the
            specified slot of the object to be built.
 
            The slot can be specified either as the name of the
            respective method, or the initialization parameter that
            would be otherwise passed to new() of the object to be
            built.
 
            Note that usually only the parser will call this
            method. Use add_wanted_slots and add_unwanted_slots for
            configuration.
 
  Example :
  Returns : TRUE if the object builder wants to populate the slot, and
            FALSE otherwise.
  Args    : the name of the slot (a string)
 
 

add_slot_value

  Title   : add_slot_value
  Usage   :
  Function: Adds one or more values to the specified slot of the object
            to be built.
 
            Naming the slot is the same as for want_slot().
 
            The object builder may further filter the content to be
            set, or even completely ignore the request.
 
            If this method reports failure, the caller should not add
            more values to the same slot. In addition, the caller may
            find it appropriate to abandon the object being built
            altogether.
 
            This implementation will allow the caller to overwrite the
            return value from want_slot(), because the slot is not
            checked against want_slot().
 
            Note that usually only the parser will call this method,
            but you may call it from anywhere if you know what you are
            doing. A derived class may be used to further manipulate
            the value to be added.
 
  Example :
  Returns : TRUE on success, and FALSE otherwise
  Args    : the name of the slot (a string)
            parameters determining the value to be set
 
                  OR
 
            alternatively, a list of slotname/value pairs in the style
            of named parameters as they would be passed to new(), where
            each element at an even index is the parameter (slot) name
            starting with a dash, and each element at an odd index is
            the value of the preceding name.
 
 

want_object

  Title   : want_object
  Usage   :
  Function: Whether or not the object builder is still interested in
            continuing with the object being built.
 
            If this method returns FALSE, the caller should not add any
            more values to slots, or otherwise risks that the builder
            throws an exception. In addition, make_object() is likely
            to return undef after this method returned FALSE.
 
            Note that usually only the parser will call this
            method. Use add_object_condition for configuration.
 
  Example :
  Returns : TRUE if the object builder wants to continue building
            the present object, and FALSE otherwise.
  Args    : none
 
 

make_object

  Title   : make_object
  Usage   :
  Function: Get the built object.
 
            This method is allowed to return undef if no value has ever
            been added since the last call to make_object(), or if
            want_object() returned FALSE (or would have returned FALSE)
            before calling this method.
 
            For an implementation that allows consecutive building of
            objects, a caller must call this method once, and only
            once, between subsequent objects to be built. I.e., a call
            to make_object implies 'end_object.'
 
  Example :
  Returns : the object that was built
  Args    : none
 
 

Implementation specific methods

These methods allow to conveniently configure this sequence object builder as to which slots are desired, and under which circumstances a sequence object should be abandoned altogether. The default mode is want_all(1), which means the builder will report all slots as wanted that the object created by the sequence factory supports.

You can add specific slots you want through add_wanted_slots(). In most cases, you will want to call want_none() before in order to relax zero acceptance through a list of wanted slots.

Alternatively, you can add specific unwanted slots through add_unwanted_slots(). In this case, you will usually want to call want_all(1) before (which is the default if you never touched the builder) to restrict unrestricted acceptance.

I.e., want_all(1) means want all slots except for the unwanted, and want_none() means only those explicitly wanted.

If a slot is in both the unwanted and the wanted list, the following rules hold. In want-all mode, the unwanted list overrules. In want-none mode, the wanted list overrides the unwanted list. If this is confusing to you, just try to avoid having slots at the same time in the wanted and the unwanted lists.

get_wanted_slots

  Title   : get_wanted_slots
  Usage   : $obj->get_wanted_slots($newval)
  Function: Get the list of wanted slots
  Example : 
  Returns : a list of strings
  Args    :
 
 

add_wanted_slot

  Title   : add_wanted_slot
  Usage   :
  Function: Adds the specified slots to the list of wanted slots.
  Example :
  Returns : TRUE
  Args    : an array of slot names (strings)
 
 

remove_wanted_slots

  Title   : remove_wanted_slots
  Usage   :
  Function: Removes all wanted slots added previously through
            add_wanted_slots().
  Example :
  Returns : the previous list of wanted slot names
  Args    : none
 
 

get_unwanted_slots

  Title   : get_unwanted_slots
  Usage   : $obj->get_unwanted_slots($newval)
  Function: Get the list of unwanted slots.
  Example : 
  Returns : a list of strings
  Args    : none
 
 

add_unwanted_slot

  Title   : add_unwanted_slot
  Usage   :
  Function: Adds the specified slots to the list of unwanted slots.
  Example :
  Returns : TRUE
  Args    : an array of slot names (strings)
 
 

remove_unwanted_slots

  Title   : remove_unwanted_slots
  Usage   :
  Function: Removes the list of unwanted slots added previously through
            add_unwanted_slots().
  Example :
  Returns : the previous list of unwanted slot names
  Args    : none
 
 

want_none

  Title   : want_none
  Usage   :
  Function: Disables all slots. After calling this method, want_slot()
            will return FALSE regardless of slot name.
 
            This is different from removed_wanted_slots() in that it
            also sets want_all() to FALSE. Note that it also resets the
            list of unwanted slots in order to avoid slots being in
            both lists.
 
  Example :
  Returns : TRUE
  Args    : none
 
 

want_all

  Title   : want_all
  Usage   : $obj->want_all($newval)
  Function: Whether or not this sequence object builder wants to
            populate all slots that the object has. Whether an object
            supports a slot is generally determined by what can()
            returns. You can add additional 'virtual' slots by calling
            add_wanted_slot.
 
            This will be ON by default. Call $obj->want_none() to
            disable all slots.
 
  Example : 
  Returns : TRUE if this builder wants to populate all slots, and
            FALSE otherwise.
  Args    : on set, new value (a scalar or undef, optional)
 
 

get_object_conditions

  Title   : get_object_conditions
  Usage   :
  Function: Get the list of conditions an object must meet in order to
            be 'wanted.' See want_object() for where this is used.
 
            Conditions in this implementation are closures (anonymous
            functions) which are passed one parameter, a hash reference
            the keys of which are equal to initialization
            paramaters. The closure must return TRUE to make the object
            'wanted.'
 
            Conditions will be implicitly ANDed.
 
  Example :
  Returns : a list of closures
  Args    : none
 
 

add_object_condition

  Title   : add_object_condition
  Usage   :
  Function: Adds a condition an object must meet in order to be 'wanted.'
            See want_object() for where this is used.
 
            Conditions in this implementation must be closures
            (anonymous functions). These will be passed one parameter,
            which is a hash reference with the sequence object
            initialization paramters being the keys.
 
            Conditions are implicitly ANDed. If you want other
            operators, perform those tests inside of one closure
            instead of multiple.  This will also be more efficient.
 
  Example :
  Returns : TRUE
  Args    : the list of conditions
 
 

remove_object_conditions

  Title   : remove_object_conditions
  Usage   :
  Function: Removes the conditions an object must meet in order to be
            'wanted.'
  Example :
  Returns : The list of previously set conditions (an array of closures)
  Args    : none
 
 

Methods to control what type of object is built

sequence_factory

  Title   : sequence_factory
  Usage   : $obj->sequence_factory($newval)
  Function: Get/set the sequence factory to be used by this object
            builder.
  Example : 
  Returns : the Bio::Factory::SequenceFactoryI implementing object to use
  Args    : on set, new value (a Bio::Factory::SequenceFactoryI
            implementing object or undef, optional)