This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/DB/GenPept, Next: Bio/DB/NCBIHelper, Prev: Bio/DB/GenBank, Up: Module List Database object interface to GenPept ************************************ NAME ==== Bio::DB::GenPept - Database object interface to GenPept SYNOPSIS ======== $gb = new Bio::DB::GenPept; $seq = $gb->get_Seq_by_id('195055'); # Unique ID # or ... $seq = $gb->get_Seq_by_acc('DEECTH'); # Accession Number my $seqio = $gb->get_Stream_by_id(['195055', 'DEECTH']); while( my $seq = $seqio->next_seq ) { print "seq is is ", $seq->display_id, "\n"; } DESCRIPTION =========== Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at NCBI, via an Entrez query. WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Batch Entrez support will likely be supported in a future version of DB::GenPept. Currently the only return format supported by NCBI Entrez for GenPept database is GenPept format, so any format specification passed to GenPept will be ignored still be forced to GenPept format (which is just GenBank format). 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Aaron Mackey, Jason Stajich ==================================== Email amackey@virginia.edu Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_params ---------- Title : get_params Usage : my %params = $self->get_params($mode) Function: Returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : a key,value pair hash Args : 'single' or 'batch' mode for retrieval default_format -------------- Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI =========================================================== get_Seq_by_id ------------- Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception get_Stream_by_acc ----------------- Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() Routines implemented by Bio::DB::NCBIHelper =========================================== get_request ----------- Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) get_Stream_by_batch ------------------- Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. get_Stream_by_id ---------------- Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries get_Stream_by_acc (2) --------------------- Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() request_format -------------- Title : request_format Usage : my $format = $self->request_format; $self->request_format($format); Function: Get/Set sequence format retrieval Returns : string representing format Args : $format = sequence format  File: pm.info, Node: Bio/DB/NCBIHelper, Next: Bio/DB/RandomAccessI, Prev: Bio/DB/GenPept, Up: Module List A collection of routines useful for queries to NCBI databases. ************************************************************** NAME ==== Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases. SYNOPSIS ======== Do not use this module directly. # get a Bio::DB::NCBIHelper object somehow my $seqio = $db->get_Stream_by_acc(['MUSIGHBA1']); foreach my $seq ( $seqio->next_seq ) { # process seq } DESCRIPTION =========== Provides a single place to setup some common methods for querying NCBI web databases. This module is just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in `postprocess_data' in this node(). 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_params ---------- Title : get_params Usage : my %params = $self->get_params($mode) Function: Returns key,value pairs to be passed to NCBI database for either 'batch' or 'single' sequence retrieval method Returns : a key,value pair hash Args : 'single' or 'batch' mode for retrieval default_format -------------- Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none get_request ----------- Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) get_Stream_by_batch ------------------- Title : get_Stream_by_batch Usage : $seq = $db->get_Stream_by_batch($ref); Function: Retrieves Seq objects from Entrez 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. postprocess_data ---------------- Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data request_format -------------- Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format  File: pm.info, Node: Bio/DB/RandomAccessI, Next: Bio/DB/SeqI, Prev: Bio/DB/NCBIHelper, Up: Module List Abstract interface for a sequence database ****************************************** NAME ==== Bio::DB::RandomAccessI - Abstract interface for a sequence database SYNOPSIS ======== # # get a database object somehow using a concrete class # $seq = $db->get_Seq_by_id('ROA1_HUMAN'); # # $seq is a Bio::Seq object # DESCRIPTION =========== This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::RandomAccessI class defines what methods a generic database class should have. At the moment it is just the ability to make Bio::Seq objects from a name (id) or a accession number. CONTACT ======= Ewan Birney originally wrote this class. Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_Seq_by_id ------------- Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception get_Seq_by_acc -------------- Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception  File: pm.info, Node: Bio/DB/SeqI, Next: Bio/DB/SwissProt, Prev: Bio/DB/RandomAccessI, Up: Module List Abstract Interface for Sequence databases ***************************************** NAME ==== Bio::DB::SeqI - Abstract Interface for Sequence databases SYNOPSIS ======== # get a Bio::DB::SeqI somehow $seq = $seqdb->get_Seq_by_id('some-id'); $seq = $seqdb->get_Seq_by_acc('some-accession-number'); @ids = $seqdb->get_all_ids(); $stream = $seqdb->get_PrimarySeq_stream(); while((my $seq = $stream->next_seq()) { # $seq is a PrimarySeqI compliant object } DESCRIPTION =========== Abstract interface for a sequence database 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 one of the Bioperl mailing lists. Your participation is much appreciated. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney ==================== Email birney@ebi.ac.uk Describe contact details here APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Methods inherieted from Bio::DB::RandomAccessI ============================================== get_Seq_by_id ------------- Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception get_Seq_by_acc -------------- Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception Methods [that were] specific for Bio::DB::SeqI ============================================== get_PrimarySeq_stream --------------------- Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq Returns : Bio::DB::SeqStreamI Args : none get_all_primary_ids ------------------- Title : get_all_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none get_Seq_by_primary_id --------------------- Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception  File: pm.info, Node: Bio/DB/SwissProt, Next: Bio/DB/UpdateableSeqI, Prev: Bio/DB/SeqI, Up: Module List Database object interface to SwissProt retrieval ************************************************ NAME ==== Bio::DB::SwissProt - Database object interface to SwissProt retrieval SYNOPSIS ======== use Bio::DB::SwissProt; $sp = new Bio::DB::SwissProt; $seq = $sp->get_Seq_by_id('P43780'); # SwissProtID # or ... $seq = $sp->get_Seq_by_acc('P43780'); # SwissProtID # can only query on SwissProtID at expasy right now # choose a different server to query $sp = new Bio::DB::SwissProt('-hostlocation' => 'canada'); $seq = $sp->get_Seq_by_id('P43780'); # SwissProtID DESCRIPTION =========== Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the SwissProt database via an expasy retrieval. Perhaps through SRS later. In order to make changes transparent we have host type (currently only expasy) and location (default to switzerland) separated out. This allows the user to pick the closest expasy mirror for running their queries. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email Jason Stajich APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Routines from Bio::DB::WebDBSeqI ================================ get_request ----------- Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) postprocess_data ---------------- Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data default_format -------------- Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none Bio::DB::SwissProt specific routines ==================================== servertype ---------- Title : servertype Usage : my $servertype = $self->servertype $self->servertype($servertype); Function: Get/Set server type Returns : string Args : server type string [optional] hostlocation ------------ Title : hostlocation Usage : my $location = $self->hostlocation() $self->hostlocation($location) Function: Set/Get Hostlocation Returns : string representing hostlocation Args : string specifying hostlocation [optional] location_url ------------ Title : location Usage : my $url = $self->location_url() Function: Get host url Returns : string representing url Args : none  File: pm.info, Node: Bio/DB/UpdateableSeqI, Next: Bio/DB/WebDBSeqI, Prev: Bio/DB/SwissProt, Up: Module List An interface for writing to a database of sequences. **************************************************** NAME ==== Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences. SYNOPSIS ======== # get a Bio::DB::UpdateableSeqI somehow eval { my ( @updatedseqs, @newseqs, @deadseqs); my $seq = $db->get_Seq_by_id('ROA1_HUMAN'); $seq->desc('a new description'); push @updatedseqs, $seq; $db->write_seq(\@updatedseqs, \@newseqs, \@deadseqs); }; if( $@ ) { print STDERR "an error when trying to write seq : $@\n"; } DESCRIPTION =========== This module seeks to provide a simple method for pushing sequence changes back to a Sequence Database - which can be an SQL compliant database, a file based database, AceDB, etc. AUTHOR ====== Jason Stajich Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://www.bioperl.org/bioperl-bugs/ APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ write_seq --------- Title : write_seq Usage : write_seq(\@updatedseqs, \@addedseqs, \@deadseqs) Function: updates sequences in first array, adds sequences in the second array, and removes sequences in the third array. Example : Returns : Args : arrays of sequence objects that must be obtained from Bio::DB::UpdateableSeqI. _add_seq -------- Title : _add_seq Usage : _add_seq($seq) Function: Adds a new sequence Example : Returns : will throw an exception if sequences accession number already exists Args : a new seq object - should have an accession number _remove_seq ----------- Title : _remove_seq Usage : _remove_seq($seq) Function: Removes an existing sequence Example : Returns : will throw an exception if sequence does not exists for the primary_id Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI _update_seq ----------- Title : _update_seq Usage : _update_seq($seq) Function: Updates a sequence Example : Returns : will throw an exception if sequence is out of sync from expected val. Args : a seq object that was retrieved from Bio::DB::UpdateableSeqI Methods inherieted from Bio::DB::RandomAccessI ============================================== get_Seq_by_id ------------- Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception get_Seq_by_acc -------------- Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception Methods inheirited from Bio::DB::SeqI ===================================== get_PrimarySeq_stream --------------------- Title : get_PrimarySeq_stream Usage : $stream = get_PrimarySeq_stream Function: Makes a Bio::DB::SeqStreamI compliant object which provides a single method, next_primary_seq Returns : Bio::DB::SeqStreamI Args : none get_all_primary_ids ------------------- Title : get_all_ids Usage : @ids = $seqdb->get_all_primary_ids() Function: gives an array of all the primary_ids of the sequence objects in the database. These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Example : Returns : an array of strings Args : none get_Seq_by_primary_id --------------------- Title : get_Seq_by_primary_id Usage : $seq = $db->get_Seq_by_primary_id($primary_id_string); Function: Gets a Bio::Seq object by the primary id. The primary id in these cases has to come from $db->get_all_primary_ids. There is no other way to get (or guess) the primary_ids in a database. The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception  File: pm.info, Node: Bio/DB/WebDBSeqI, Next: Bio/DBLinkContainerI, Prev: Bio/DB/UpdateableSeqI, Up: Module List Object Interface to generalize Web Databases for retrieving sequences *********************************************************************** NAME ==== Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences SYNOPSIS ======== # get a WebDBSeqI object somehow # assuming it is a nucleotide db my $seq = $db->get_Seq_by_id('ROA1_HUMAN') DESCRIPTION =========== Provides core set of functionality for connecting to a web based database for retriving sequences. Users wishing to add another Web Based Sequence Dabatase will need to extend this class (see Bio::DB::SwissProt or Bio::DB::NCBIHelper for examples) and implement the get_request method which returns a HTTP::Request for the specified uids (accessions, ids, etc depending on what query types the database accepts). 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_Seq_by_id ------------- Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') Function: Gets a Bio::Seq object by its name Returns : a Bio::Seq object Args : the id (as a string) of a sequence Throws : "id does not exist" exception get_Seq_by_acc -------------- Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('X77802'); Function: Gets a Bio::Seq object by accession number Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception get_request ----------- Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc) get_Stream_by_id ---------------- Title : get_Stream_by_id Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] ); Function: Gets a series of Seq objects by unique identifiers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of unique identifiers for the desired sequence entries get_Stream_by_acc ----------------- Title : get_Stream_by_acc Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]); Function: Gets a series of Seq objects by accession numbers Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession numbers for the desired sequence entries Note : For GenBank, this just calls the same code for get_Stream_by_id() default_format -------------- Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none request_format -------------- Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format get_seq_stream -------------- Title : get_seq_stream Usage : my $seqio = $self->get_seq_sream(%qualifiers) Function: builds a url and queries a web db Returns : a Bio::SeqIO stream capable of producing sequence Args : %qualifiers = a hash qualifiers that the implementing class will process to make a url suitable for web querying url_base_address ---------------- Title : url_base_address Usage : my $address = $self->url_base_address or $self->url_base_address($address) Function: Get/Set the base URL for the Web Database Returns : Base URL for the Web Database Args : $address - URL for the WebDatabase proxy ----- Title : proxy Usage : $httpproxy = $db->proxy('http') or $db->proxy(['http','ftp'], 'http://myproxy' ) Function: Get/Set a proxy for use of proxy Returns : a string indicating the proxy Args : $protocol : an array ref of the protocol(s) to set/get $proxyurl : url of the proxy to use for the specified protocol retrieval_type -------------- Title : retrieval_type Usage : $self->retrieval_type($type); my $type = $self->retrieval_type Function: Get/Set a proxy for retrieval_type (io_string or tempfile) Returns : string representing retrieval type Args : $value - the value to store url_params ---------- Title : url_params Usage : my $params = $self->url_params or $self->url_params($params) Function: Get/Set the URL parameters for the Web Database Returns : url parameters for Web Database Args : $params - parameters to be appended to the URL for the WebDatabase ua -- Title : ua Usage : my $ua = $self->ua or $self->ua($ua) Function: Get/Set a LWP::UserAgent for use Returns : reference to LWP::UserAgent Object Args : $ua - must be a LWP::UserAgent postprocess_data ---------------- Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data  File: pm.info, Node: Bio/DBLinkContainerI, Next: Bio/Factory/DriverFactory, Prev: Bio/DB/WebDBSeqI, Up: Module List Abstract interface for any object wanting to use database cross references **************************************************************************************************** NAME ==== Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references SYNOPSIS ======== # get an objects containing database cross reference foreach $obj ( @objs ) { if( $obj->isa('Bio::DBLinkContainerI') ) { foreach $dblink ( $obj->each_DBLink() ) { # do stuff } } } DESCRIPTION =========== This interface defines the functions one can expect for any object wanting to use database cross-references. This class does not actually provide any implemention, it just provides the definitions of what methods one can call. The database cross-references are implemented as *Note Bio/Annotation/DBLink: Bio/Annotation/DBLink, objects. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Heikki Lehvaslaiho =========================== Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ each_DBLink ----------- Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : an array of Bio::Annotation::DBLink objects Args : none  File: pm.info, Node: Bio/Factory/DriverFactory, Next: Bio/Factory/SeqAnalysisParserFactory, Prev: Bio/DBLinkContainerI, Up: Module List Base class for factory classes loading drivers ********************************************** NAME ==== Bio::Factory::DriverFactory - Base class for factory classes loading drivers SYNOPSIS ======== #this class is not instantiable DESCRIPTION =========== This a base class for factory classes that load drivers. Normally, you don't instantiate this class directly. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email Jason Stajich APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ register_driver --------------- Title : register_driver Usage : $factory->register_driver("genscan", "Bio::Tools::Genscan"); Function: Registers a driver a factory class should be able to instantiate. This method can be called both as an instance and as a class method. Returns : Args : Key of the driver (string) and the module implementing the driver (string). driver_table ------------ Title : driver_table Usage : $table = $factory->driver_table(); Function: Returns a reference to the hash table storing associations of methods with drivers. You use this table to look up registered methods (keys) and drivers (values). In this implementation the table is class-specific and therefore shared by all instances. You can override this in a derived class, but note that this method can be called both as an instance and a class method. This will be the table used by the object internally. You should definitely know what you're doing if you modify the table's contents. Modifications are shared by _all_ instances, those present and those yet to be created. Returns : A reference to a hash table. Args : get_driver ---------- Title : get_driver Usage : $module = $factory->get_driver("genscan"); Function: Returns the module implementing a driver registered under the given key. Example : Returns : A string. Args : Key of the driver (string). _load_module ------------ Title : _load_module Usage : $self->_load_module("Bio::Tools::Genscan"); Function: Loads up (like use) a module at run time on demand. Example : Returns : TRUE on success Args :  File: pm.info, Node: Bio/Factory/SeqAnalysisParserFactory, Next: Bio/Factory/SeqAnalysisParserFactoryI, Prev: Bio/Factory/DriverFactory, Up: Module List class capable of creating SeqAnalysisParserI compliant parsers **************************************************************************** NAME ==== Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers SYNOPSIS ======== # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # find out the methods it knows about print "registered methods: ", join(', ', keys($factory->driver_table())), "\n"; # obtain a parser object $parser = $factory->get_parser(-input=>$inputobj, -params=>[@params], -method => $method); # $parser is an object implementing Bio::SeqAnalysisParserI # annotate sequence with features produced by parser while(my $feat = $parser->next_feature()) { $seq->add_SeqFeature($feat); } DESCRIPTION =========== This is a factory class capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind this class and the interface it implements (Bio::Factory::SeqAnalysisParserFactoryI) is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqAnalysisParserI for more documentation of this concept. You can always find out the methods an instance of this class knows about by the way given in the SYNOPSIS section. By default, and assuming that the documentation is up-to-date, this will comprise of genscan, mzef, estscan, blast, hmmer, gff, and sim4 (all case-insensitive). 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp, Jason Stajich =================================== Email Hilmar Lapp , Jason Stajich APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_parser ---------- Title : get_parser Usage : $factory->get_parser(-input=>$inputobj, [ -params=>[@params] ], -method => $method) Function: Creates and returns a parser object for the given input and method. Both file names and streams (filehandles) are allowed. Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. Example : Returns : A Bio::SeqAnalysisParserI implementing object. Exception if creation of the parser object fails. Args : B - object/file where analysis results are coming from, B - parameter to use when parsing/running analysis B - method of analysis  File: pm.info, Node: Bio/Factory/SeqAnalysisParserFactoryI, Next: Bio/Index/Abstract, Prev: Bio/Factory/SeqAnalysisParserFactory, Up: Module List interface describing objects capable of creating SeqAnalysisParserI compliant parsers *************************************************************************************************** NAME ==== Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers SYNOPSIS ======== # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object $parser = $factory->get_parser(-input=>$inputobj, -params=>[@params], -method => $method); # $parser is an object implementing Bio::SeqAnalysisParserI # annotate sequence with features produced by parser while(my $feat = $parser->next_feature()) { $seq->add_SeqFeature($feat); } DESCRIPTION =========== This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqAnalysisParserI for more documentation of this concept. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp, Jason Stajich =================================== Email Hilmar Lapp , Jason Stajich APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_parser ---------- Title : get_parser Usage : $factory->get_parser(-input=>$inputobj, [ -params=>[@params] ], -method => $method) Function: Creates and returns a parser object for the given input and method. The type of input which is suitable depends on the implementation, but a good-style implementation should allow both file names and streams (filehandles). A particular implementation may not be able to create a parser for the requested method. In this case it shall return undef. Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. An implementation of this interface should make this argument optional. Example : Returns : A Bio::SeqAnalysisParserI implementing object. Args : B - object/file where analysis results are coming from, B - parameter to use when parsing/running analysis B - method of analysis  File: pm.info, Node: Bio/Index/Abstract, Next: Bio/Index/AbstractSeq, Prev: Bio/Factory/SeqAnalysisParserFactoryI, Up: Module List Abstract interface for indexing a flat file ******************************************* NAME ==== Bio::Index::Abstract - Abstract interface for indexing a flat file SYNOPSIS ======== You should not be using this module directly USING DB_FILE ============= To use DB_File and not SDBM for this index, pass the value: -dbm_package => 'DB_File' to new (see below). DESCRIPTION =========== This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch). This object is the guts to the mechanism, which will be used by the specific objects inheriting from it. 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney, James Gilbert =================================== Email - birney@sanger.ac.uk, jgrg@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore). new --- Usage : $index = Bio::Index::Abstract->new( -filename => $dbm_file, -write_flag => 0, -dbm_package => 'DB_File', -verbose => 0); Function: Returns a new index object. If filename is specified, then open_dbm() is immediately called. Bio::Index::Abstract->new() will usually be called directly only when opening an existing index. Returns : A new index object Args : -filename The name of the dbm index file. -write_flag TRUE if write access to the dbm file is needed. -dbm_package The Perl dbm module to use for the index. -verbose Print debugging output to STDERR if TRUE. filename -------- Title : filename Usage : $value = $self->filename(); $self->filename($value); Function: Gets or sets the name of the dbm index file. Returns : The current value of filename Args : Value of filename if setting, or none if getting the value. write_flag ---------- Title : write_flag Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which is wether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if getting the value. dbm_package ----------- Usage : $value = $self->dbm_package(); $self->dbm_package($value); Function: Gets or sets the name of the Perl dbm module used. If the value is unset, then it returns the value of the package variable $USE_DBM_TYPE or if that is unset, then it chooses the best available dbm type, choosing 'DB_File' in preference to 'SDBM_File'. Bio::Abstract::Index may work with other dbm file types. Returns : The current value of dbm_package Args : Value of dbm_package if setting, or none if getting the value. db -- Title : db Usage : $index->db Function: Returns a ref to the hash which is tied to the dbm file. Used internally when adding and retrieving data from the database. Example : $db = $index->db(); $db->{ $some_key } = $data $data = $index->db->{ $some_key }; Returns : ref to HASH Args : NONE get_stream ---------- Title : get_stream Usage : $stream = $index->get_stream( $id ); Function: Returns a file handle with the file pointer at the approprite place This provides for a way to get the actual file contents and not an object WARNING: you must parse the record deliminter *yourself*. Abstract wont do this for you So this code $fh = $index->get_stream($myid); while( <$fh> ) { # do something } will parse the entire file if you don't put in a last statement in, like while( <$fh> ) { /^\/\// && last; # end of record # do something } Returns : A filehandle object Args : string represents the accession number Notes : This method should not be used without forethought open_dbm -------- Usage : $index->open_dbm() Function: Opens the dbm file associated with the index object. Write access is only given if explicitly asked for by calling new(-write => 1) or having set the write_flag(1) on the index object. The type of dbm file opened is that returned by dbm_package(). The name of the file to be is opened is obtained by calling the filename() method. Example : $index->_open_dbm() Returns : 1 on success _version -------- Title : _version Usage : $type = $index->_version() Function: Returns a string which identifes the version of an index module. Used to permanently identify an index file as having been created by a particular version of the index module. Must be provided by the sub class Example : Returns : Args : none _code_base ---------- Title : _code_base Usage : $code = $db->_code_base(); Function: Example : Returns : Code package to be used with this Args : _type_and_version ----------------- Title : _type_and_version Usage : Called by _initalize Function: Checks that the index opened is made by the same index module and version of that module that made it. If the index is empty, then it adds the information to the database. Example : Returns : 1 or exception Args : none _check_file_sizes ----------------- Title : _check_file_sizes Usage : $index->_check_file_sizes() Function: Verifies that the files listed in the database are the same size as when the database was built, or throws an exception. Called by the new() function. Example : Returns : 1 or exception Args : make_index ---------- Title : make_index Usage : $index->make_index( FILE_LIST ) Function: Takes a list of file names, checks that they are all fully qualified, and then calls _filename() on each. It supplies _filename() with the name of the file, and an integer which is stored with each record created by _filename(). Can be called multiple times, and can be used to add to an existing index file. Example : $index->make_index( '/home/seqs1', '/home/seqs2', '/nfs/pub/big_db' ); Returns : Number of files indexed Args : LIST OF FILES _filename --------- Title : _filename Usage : $index->_filename( FILE INT ) Function: Indexes the file Example : Returns : Args : _file_handle ------------ Title : _file_handle Usage : $fh = $index->_file_handle( INT ) Function: Returns an open filehandle for the file index INT. On opening a new filehandle it caches it in the @{$index->_filehandle} array. If the requested filehandle is already open, it simply returns it from the array. Example : $fist_file_indexed = $index->_file_handle( 0 ); Returns : ref to a filehandle Args : INT _file_count ----------- Title : _file_count Usage : $index->_file_count( INT ) Function: Used by the index building sub in a sub class to track the number of files indexed. Sets or gets the number of files indexed when called with or without an argument. Example : Returns : INT Args : INT add_record ---------- Title : add_record Usage : $index->add_record( $id, @stuff ); Function: Calls pack_record on @stuff, and adds the result of pack_record to the index database under key $id. If $id is a reference to an array, then a new entry is added under a key corresponding to each element of the array. Example : $index->add_record( $id, $fileNumber, $begin, $end ) Returns : TRUE on success or FALSE on failure Args : ID LIST pack_record ----------- Title : pack_record Usage : $packed_string = $index->pack_record( LIST ) Function: Packs an array of scalars into a single string joined by ASCII 034 (which is unlikely to be used in any of the strings), and returns it. Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end ) Returns : STRING or undef Args : LIST unpack_record ------------- Title : unpack_record Usage : $index->unpack_record( STRING ) Function: Splits the sting provided into an array, splitting on ASCII 034. Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} ) Returns : A 3 element ARRAY Args : STRING containing ASCII 034 DESTROY ------- Title : DESTROY Usage : Called automatically when index goes out of scope Function: Closes connection to database and handles to sequence files Returns : NEVER Args : NONE