Bio::Seq::SeqBuilder man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::Seq::SeqBuilder(3User Contributed Perl DocumentatiBio::Seq::SeqBuilder(3)

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)

perl v5.14.1			  2011-07-22	       Bio::Seq::SeqBuilder(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net