This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/Index/AbstractSeq, Next: Bio/Index/EMBL, Prev: Bio/Index/Abstract, Up: Module List Base class for AbstractSeq s **************************** NAME ==== Bio::Index::AbstractSeq - Base class for AbstractSeq s SYNOPSIS ======== # Make a new sequence file indexing package package MyShinyNewIndexer; use Bio::Index::AbstractSeq; @ISA = ('Bio::Index::AbstractSeq'); # Now provide the necessary methods... DESCRIPTION =========== Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and provides a Bio::DB::SeqI interface. 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 ==================== 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 _ SEE ALSO ======== Bio::Index::Abstract - Module which Bio::Index::AbstractSeq inherits off, which provides dbm indexing for flat files (which are not necessarily sequence files). _file_format ------------ Title : _file_format Usage : $self->_file_format Function: Derived classes should override this method (it throws an exception here) to give the file format of the files used Example : Returns : Args : fetch ----- Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID _get_SeqIO_object ----------------- Title : _get_SeqIO_object Usage : $index->_get_SeqIO_object( $file ) Function: Returns a Bio::SeqIO object for the file Example : $seq = $index->_get_SeqIO_object( 0 ) Returns : Bio::SeqIO object Args : File number (an integer) get_Seq_by_id ------------- Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id() Function: retrieves a sequence object, identically to ->fetch, but here behaving as a Bio::DB::BioSeqI Returns : new Bio::Seq object Args : string represents the id get_Seq_by_acc -------------- Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc() Function: retrieves a sequence object, identically to ->fetch, but here behaving as a Bio::DB::BioSeqI Returns : new Bio::Seq object Args : string represents the accession number 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_primary_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 : primary id (as a string) Throws : "acc does not exist" exception  File: pm.info, Node: Bio/Index/EMBL, Next: Bio/Index/Fasta, Prev: Bio/Index/AbstractSeq, Up: Module List Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). ************************************************************************************************* NAME ==== Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). SYNOPSIS ======== # Complete code for making an index for several # EMBL files use Bio::Index::EMBL; my $Index_File_Name = shift; my $inx = Bio::Index::EMBL->new($Index_File_Name, 'WRITE'); $inx->make_index(@ARGV); # Print out several sequences present in the index # in Fasta format use Bio::Index::EMBL; my $Index_File_Name = shift; my $inx = Bio::Index::EMBL->new($Index_File_Name); my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $out->write_seq($seq); } # alternatively my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc); DESCRIPTION =========== Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing EMBL files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system. FEED_BACK ========= 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 ==================== Email - birney@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _index_file ----------- Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index EMBL format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args : _file_format ------------ Title : _file_format Usage : Internal function for indexing system Function: Provides file format for this database Example : Returns : Args :  File: pm.info, Node: Bio/Index/Fasta, Next: Bio/Index/GenBank, Prev: Bio/Index/EMBL, Up: Module List Interface for indexing (multiple) fasta files ********************************************* NAME ==== Bio::Index::Fasta - Interface for indexing (multiple) fasta files SYNOPSIS ======== # Complete code for making an index for several # fasta files use Bio::Index::Fasta; my $Index_File_Name = shift; my $inx = Bio::Index::Fasta->new( -filename => $Index_File_Name, -write_flag => 1); $inx->make_index(@ARGV); # Print out several sequences present in the index # in Fasta format use Bio::Index::Fasta; my $Index_File_Name = shift; my $inx = Bio::Index::Fasta->new($Index_File_Name); my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $out->write_seq($seq); } # or, alternatively my $seq = $inx->get_Seq_by_id($id); #identical to fetch DESCRIPTION =========== Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fasta files, and retrieving the sequence from them. Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used a a Sequence database for other parts of bioperl FEED_BACK ========= 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 - James Gilbert ====================== Email - jgrg@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _file_format ------------ Title : _file_format Function: The file format for this package, which is needed by the SeqIO system when reading the sequence. Returns : 'Fasta' _index_file ----------- Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index FASTA format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args : id_parser --------- Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Useful for (for instance) specifying a different parser for different flavours of FASTA file. Returns \&default_id_parser (see below) if not set. If you supply your own id_parser subroutine, then it should expect a fasta description line. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE default_id_parser ----------------- Title : default_id_parser Usage : $id = default_id_parser( $header ) Function: The default Fasta ID parser for Fasta.pm Returns $1 from applying the regexp /^>\s*(\S+)/ to $header. Returns : ID string Args : a fasta header line string  File: pm.info, Node: Bio/Index/GenBank, Next: Bio/Index/SwissPfam, Prev: Bio/Index/Fasta, Up: Module List Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). *********************************************************************************** NAME ==== Bio::Index::GenBank - Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). SYNOPSIS ======== # Complete code for making an index for several # GenBank files use Bio::Index::GenBank; my $Index_File_Name = shift; my $inx = Bio::Index::GenBank->new($Index_File_Name, 'WRITE'); $inx->make_index(@ARGV); # Print out several sequences present in the index # in gcg format use Bio::Index::GenBank; my $Index_File_Name = shift; my $inx = Bio::Index::GenBank->new($Index_File_Name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object print $seq->layout('GCG'); } # alternatively my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc); DESCRIPTION =========== Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing GenBank files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system. FEED_BACK ========= 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 ==================== Email - birney@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _index_file ----------- Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index GenBank format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args : _file_format ------------ Title : _file_format Usage : Internal function for indexing system Function: Provides file format for this database Example : Returns : Args :  File: pm.info, Node: Bio/Index/SwissPfam, Next: Bio/Index/Swissprot, Prev: Bio/Index/GenBank, Up: Module List Interface for indexing swisspfam files ************************************** NAME ==== Bio::Index::SwissPfam - Interface for indexing swisspfam files SYNOPSIS ======== use Bio::Index::SwissPfam; my $Index_File_Name = shift; my $inx = Bio::Index::SwissPfam->new($Index_File_Name, 'WRITE'); $inx->make_index(@ARGV); use Bio::Index::SwissPfam; my $Index_File_Name = shift; my $inx = Bio::Index::SwissPfam->new($Index_File_Name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns stream while( <$seq> ) { if(/^>/) { print; last; } } } DESCRIPTION =========== SwissPfam is one of the flat files released with Pfam. This modules provides a way of indexing this module. Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing SwissPfam files. Only retrieves FileStreams at the moment. Once we have something better (ie, an object!), will use that. Heavily snaffled from James Gilbert's Fasta system. FEED_BACK ========= 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 ==================== Email - birney@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _index_file ----------- Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index swisspfam format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args : fetch ----- Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID  File: pm.info, Node: Bio/Index/Swissprot, Next: Bio/LiveSeq/AARange, Prev: Bio/Index/SwissPfam, Up: Module List Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). *************************************************************************************** NAME ==== Bio::Index::Swissprot - Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS ======== # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; my $Index_File_Name = shift; my $inx = Bio::Index::Swissprot->new($Index_File_Name, 'WRITE'); $inx->make_index(@ARGV); # Print out several sequences present in the index # in gcg format use Bio::Index::Swissprot; use Bio::SeqIO; my $out = Bio::SeqIO->new( '-format' => 'gcg', -fh => \*STDOUT ); my $Index_File_Name = shift; my $inx = Bio::Index::Swissprot->new($Index_File_Name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $out->write_seq($seq); } # alternatively my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc); DESCRIPTION =========== Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing Swissprot files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system. FEED_BACK ========= 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 - Ewan Birney ==================== Email - birney@sanger.ac.uk (Swissprot adaption: lorenz@ist.org) APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _index_file ----------- Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index Swissprot format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args : _file_format ------------ Title : _file_format Usage : Internal function for indexing system Function: Provides file format for this database Example : Returns : Args :  File: pm.info, Node: Bio/LiveSeq/AARange, Next: Bio/LiveSeq/Chain, Prev: Bio/Index/Swissprot, Up: Module List AARange abstract class for LiveSeq ********************************** NAME ==== Bio::LiveSeq::AARange - AARange abstract class for LiveSeq SYNOPSIS ======== #documentation needed DESCRIPTION =========== This is used as possible parent for aminoacid range object classes. Or it can be used straight away to define aminoacid ranges. The idea is that the ranges defined are attached to a Translation object and they refer to its coordinate-system when they are first created (via the new() method). When they are created they are anyway linked to the underlying DNA LiveSeq by way of the LiveSeq labels. This allows to preserve the ranges even if the numbering changes in the Translation due to deletions or insertions. The protein sequence associated with the AARange can be accessed via the usual seq() or subseq() methods. The start and end of the AARange in protein coordinate system can be fetched with aa_start() and aa_end() methods. Note: the behaviour of these methods would be influenced by the coordinate_start set in the corresponding Translation object. This can be desirable but can also lead to confusion if the coordinate_start had been changed and the original position of the AARange was to be retrieved. start() and end() methods of the AARange will point to the labels identifying the first nucleotide of the first and last triplet coding for the start and end of the AminoAcidRange. The underlying nucleotide sequence of the AARange can be retrieved with the labelsubseq() method. This would retrieve the whole DNA sequence, including possible introns. This is called "DNA_sequence". To fetch the nucleotide sequence of the Transcript, without introns, the labelsubseq() of the attached Transcript (the Transcript the Translation comes from) has to be accessed. This is called "cDNA_sequence". Here are the operations to retrieve these latter two kinds of sequences: $startlabel=$AARange->start; $endtripletlabel=$AARange->end; $endlabel=$AARange->{'seq'}->label(3,$endtripletlabel,$AARange->strand); $dnaseq=$AARange->labelsubseq($startlabel,undef,$endlabel)); $cdnaseq=$AARange->get_Transcript->labelsubseq($startlabel,undef,$endlabel); To simplify, these operations have been included in two additional methods: dna_seq() and cdna_seq(). These would return the whole sequence, as in the examples above. But the above general scheme can be used by specifying different labels, to retrieve hypothetical subsequences of interest. AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net 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 _ new === Title : new Usage : $aarange = Bio::LiveSeq::AARange->new(-translation => $obj_ref, -start => $beginaa, -end => $endaa, -name => "ABCD", -description => "DCBA", -translength => $length); Function: generates a new AminoAcidRange LiveSeq object Returns : reference to a new object of class AARange Errorcode -1 Args : two positions in AminoAcid coordinate numbering an object reference specifying to which translation the aminoacid ranges refer to a name and a description (optional) an optional "translength" argument: this can be given when a lot of AARanges are to be created at the same time for the same Translation object, calculating it with $translation->length This would increase the speed, avoiding the new() function to calculate everytime the same length again and again for every obj. get_Transcript -------------- Title : valid Usage : $transcript = $obj->get_Transcript() Function: retrieves the reference to the object of class Transcript (if any) attached to a LiveSeq object Returns : object reference Args : none get_Translation --------------- Title : valid Usage : $translation = $obj->get_Translation() Function: retrieves the reference to the object of class Translation (if any) attached to a LiveSeq object Returns : object reference Args : none aa_start -------- Title : aa_start Usage : $end = $aarange->aa_start() Returns : integer (position, according to Translation coordinate system) of the start of an AminoAcidRange object Args : none aa_end ------ Title : aa_end Usage : $end = $aarange->aa_end() Returns : integer (position, according to Translation coordinate system) of the end of an AminoAcidRange object Args : none dna_seq ------- Title : dna_seq Usage : $end = $aarange->dna_seq() Returns : the sequence at DNA level of the entire AminoAcidRange this would include introns (if present) Args : none cdna_seq -------- Title : cdna_seq Usage : $end = $aarange->cdna_seq() Returns : the sequence at cDNA level of the entire AminoAcidRange i.e. this is the part of the Transcript that codes for the AminoAcidRange. It would be composed just of exonic DNA. Args : none  File: pm.info, Node: Bio/LiveSeq/Chain, Next: Bio/LiveSeq/ChainI, Prev: Bio/LiveSeq/AARange, Up: Module List DoubleChain DataStructure for Perl ********************************** NAME ==== Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl SYNOPSIS ======== #documentation needed DESCRIPTION =========== This is a general purpose module (that's why it's not in object-oriented form) that introduces a novel datastructure in PERL. It implements the "double linked chain". The elements of the chain can contain basically everything. From chars to strings, from object references to arrays or hashes. It is used in the LiveSequence project to create a dynamical DNA sequence, easier to manipulate and change. It's use is mainly for sequence variation analysis but it could be used - for example - in e-cell projects. The Chain module in itself doesn't have any biological bias, so can be used for any programming purpose. Each element of the chain (with the exclusion of the first and the last of the chain) is connected to other two elements (the PREVious and the NEXT one). There is no absolute position (like in an array), hence if positions are important, they need to be computed (methods are provided). Otherwise it's easy to keep track of the elements with their "LABELs". There is one LABEL (think of it as a pointer) to each ELEMENT. The labels won't change after insertions or deletions of the chain. So it's always possible to retrieve an element even if the chain has been modified by successive insertions or deletions. From this the high potential profit for bioinformatics: dealing with sequences in a way that doesn't have to rely on positions, without the need of constantly updating them if the sequence changes, even dramatically. AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net 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 _ _updown_chain2string Title : chain2string Usage : $string = Bio::LiveSeq::Chain::chain2string("down",$chain,6,9) Function: reads the contents of the chain, outputting a string Returns : a string Examples: : down_chain2string($chain) -> all the chain from begin to end : down_chain2string($chain,6) -> from 6 to the end : down_chain2string($chain,6,4) -> from 6, going on 4 elements : down_chain2string($chain,6,"",10) -> from 6 to 10 : up_chain2string($chain,10,"",6) -> from 10 to 6 upstream Defaults: start=first element; if len undef, goes to last if last undef, goes to end if last defined, it overrides len (undefining it) Error code: -1 Args : "up"||"down" as first argument to specify the reading direction reference (to the chain) [first] [len] [last] optional integer arguments to specify how much and from (and to) where to read ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- _updown_labels -------------- Title : labels Usage : @labels = Bio::LiveSeq::Chain::_updown_labels("down",$chain,4,16) Function: returns all the labels in a chain or those between two specified ones (termed "first" and "last") Returns : a reference to an array containing the labels Args : "up"||"down" as first argument to specify the reading direction reference (to the chain) [first] [last] (integer for the starting and eneding labels) start ----- Title : start Usage : $start = Bio::LiveSeq::Chain::start() Returns : the label marking the start of the chain Errorcode: -1 Args : none end --- Title : end Usage : $end = Bio::LiveSeq::Chain::end() Returns : the label marking the end of the chain Errorcode: -1 Args : none label_exists ------------ Title : label_exists Usage : $check = Bio::LiveSeq::Chain::label_exists($chain,$label) Function: It checks if a label is defined, i.e. if an element is there or is not there anymore Returns : 1 if the label exists, 0 if it is not there, -1 error Errorcode: -1 Args : reference to the chain, integer down_get_pos_of_label --------------------- Title : down_get_pos_of_label Usage : $position = Bio::LiveSeq::Chain::down_get_pos_of_label($chain,$label,$first) Function: returns the position of $label counting from $first, i.e. taking $first as 1 of coordinate system. If $first is not specified it will count from the start of the chain. Returns : Errorcode: 0 Args : reference to the chain, integer (the label of interest) optional: integer (a different label that will be taken as the first one, i.e. the one to count from) Note: It counts "downstream". To proceed backward use up_get_pos_of_label down_subchain_length -------------------- Title : down_subchain_length Usage : $length = Bio::LiveSeq::Chain::down_subchain_length($chain,$first,$last) Function: returns the length of the chain between the labels "first" and "last", included Returns : integer Errorcode: 0 Args : reference to the chain, integer, integer Note: It counts "downstream". To proceed backward use up_subchain_length invert_chain ------------ Title : invert_chain Usage : $errorcode=Bio::LiveSeq::Chain::invert_chain($chain) Function: completely inverts the order of the chain elements; begin is swapped with end and all links updated (PREV&NEXT fields swapped) Returns : 1 if all OK, 0 if errors Errorcode: 0 Args : reference to the chain down_get_value_at_pos --------------------- Title : down_get_value_at_pos Usage : $value = Bio::LiveSeq::Chain::down_get_value_at_pos($chain,$position,$first) Function: used to access the value of the chain at a particular position instead than directly with a label pointer. It will count the position from the start of the chain or from the label $first, if $first is specified Returns : whatever is stored in the element of the chain Errorcode: 0 Args : reference to the chain, integer, [integer] Note: It works "downstream". To proceed backward use up_get_value_at_pos down_set_value_at_pos --------------------- Title : down_set_value_at_pos Usage : $errorcode = Bio::LiveSeq::Chain::down_set_value_at_pos($chain,$newvalue,$position,$first) Function: used to store a new value inside an element of the chain at a particular position instead than directly with a label pointer. It will count the position from the start of the chain or from the label $first, if $first is specified Returns : 1 Errorcode: 0 Args : reference to the chain, newvalue, integer, [integer] (newvalue can be: integer, string, object reference, hash ref) Note: It works "downstream". To proceed backward use up_set_value_at_pos Note2: If the $newvalue is undef, it will delete the contents of the element but it won't remove the element from the chain. down_set_value_at_label ----------------------- Title : down_set_value_at_label Usage : $errorcode = Bio::LiveSeq::Chain::down_set_value_at_label($chain,$newvalue,$label) Function: used to store a new value inside an element of the chain defined by its label. Returns : 1 Errorcode: 0 Args : reference to the chain, newvalue, integer (newvalue can be: integer, string, object reference, hash ref) Note: It works "downstream". To proceed backward use up_set_value_at_label Note2: If the $newvalue is undef, it will delete the contents of the element but it won't remove the element from the chain. down_get_value_at_label ----------------------- Title : down_get_value_at_label Usage : $value = Bio::LiveSeq::Chain::down_get_value_at_label($chain,$label) Function: used to access the value of the chain from one element defined by its label. Returns : whatever is stored in the element of the chain Errorcode: 0 Args : reference to the chain, integer Note: It works "downstream". To proceed backward use up_get_value_at_label down_get_label_at_pos --------------------- Title : down_get_label_at_pos Usage : $label = Bio::LiveSeq::Chain::down_get_label_at_pos($chain,$position,$first) Function: used to retrieve the label of an an element of the chain at a particular position. It will count the position from the start of the chain or from the label $first, if $first is specified Returns : integer Errorcode: 0 Args : reference to the chain, integer, [integer] Note: It works "downstream". To proceed backward use up_get_label_at_pos _praepostinsert_array --------------------- Title : _praepostinsert_array Usage : ($insbegin,$insend) = Bio::LiveSeq::Chain::_praepostinsert_array($chainref,"post",$arrayref,$position) Function: the elements of the array specified by $arrayref are inserted (creating a new subchain) in the chain specified by $chainref, before or after (depending on the "prae"||"post" keyword passed as second argument) the specified position. Returns : two labels: the first and the last of the inserted subchain Defaults: if no position is specified, the new chain will be inserted after (post) the first element of the chain Errorcode: 0 Args : chainref, "prae"||"post", arrayref, integer (position) is_downstream ============= Title : is_downstream Usage : Bio::LiveSeq::Chain::is_downstream($chainref,$firstlabel,$secondlabel) Function: checks if SECONDlabel follows FIRSTlabel It runs downstream the elements of the chain from FIRST searching for SECOND. Returns : 1 if SECOND is found /after/ FIRST; 0 otherwise (i.e. if it reaches the end of the chain without having found it) Errorcode -1 Args : two labels (integer) is_upstream =========== Title : is_upstream Usage : Bio::LiveSeq::Chain::is_upstream($chainref,$firstlabel,$secondlabel) Function: checks if SECONDlabel follows FIRSTlabel It runs upstream the elements of the chain from FIRST searching for SECOND. Returns : 1 if SECOND is found /after/ FIRST; 0 otherwise (i.e. if it reaches the end of the chain without having found it) Errorcode -1 Args : two labels (integer) check_chain ----------- Title : check_chain Usage : @errorcodes = Bio::LiveSeq::Chain::check_chain() Function: a wraparound to a series of check for consistency of the chain It will check for boundaries, size, backlinking and forwardlinking Returns : array of 4 warn codes, each can be 1 (all ok) or 0 (something wrong) Errorcode: 0 Args : none Note : this is slow and through. It is not really needed. It is mostly a code-developer tool. splice_chain ------------ Title : splice_chain Usage : @errorcodes = Bio::LiveSeq::Chain::splice_chain($chainref,$first,$length,$last) Function: removes the elements designated by FIRST and LENGTH from a chain. The chain shrinks accordingly. If LENGTH is omitted, removes everything from FIRST onward. If END is specified, LENGTH is ignored and instead the removal occurs from FIRST to LAST. Returns : the elements removed as a string Errorcode: -1 Args : chainref, integer, integer, integer array2chain ----------- Title : array2chain Usage : $chainref = Bio::LiveSeq::Chain::array2chain($arrayref,$offset) Function: creation of a double linked chain from an array Returns : reference to a hash containing the chain Defaults: OFFSET defaults to 1 if undef Error code: 0 Args : a reference to an array containing the elements to be chainlinked an optional integer > 0 (this will be the starting count for the chain labels instead than having them begin from "1")  File: pm.info, Node: Bio/LiveSeq/ChainI, Next: Bio/LiveSeq/DNA, Prev: Bio/LiveSeq/Chain, Up: Module List Double linked chain data structure ********************************** NAME ==== Bio::LiveSeq::ChainI - Double linked chain data structure SYNOPSIS ======== #documentation needed DESCRIPTION =========== This class generates and manipulates generic double linked list, chain, that can be used to manage biological sequences. The advantages over strings or plain arrays is the ease of tracking changes (mutations) in the elements (sequence). The other side of the coin is that these structures need consideraly more memory, but that is cheap and constantly inceasing resource in computers. 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 - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net 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 _ new Title : new Usage : $chain = Bio::LiveSeq::ChainI->new(-string => "thequickbrownfoxjumpsoverthelazydog", -offset => 3 ); OR $chain = Bio::LiveSeq::ChainI->new(-array => \@array, -offset => 3 ); Function: generates a new Bio::LiveSeq:ChainI Returns : a new Chain Args : string OR arrayreference AND optional offset to create element labels =cut ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- sub new { my ($thing, %args) = @_; my $class = ref($thing) || $thing; my $obj; if ($args{-string}) { $obj = $thing->string2chain($args{-string}, $args{-offset}); } elsif ($args{-array}) { $obj = $thing->array2chain($args{-array}, $args{-offset}); } else { croak "$class not initialized properly"; } $obj = bless $obj, $class; return $obj; } # added as of 1.9 sub string2chain { shift @_; # so that it doesn't pass the object reference return Bio::LiveSeq::Chain::string2chain(@_); } sub array2chain { shift @_; # so that it doesn't pass the object reference return Bio::LiveSeq::Chain::array2chain(@_); } # sub chain2string { croak "ambiguous method call. Explicit down_ or up_"; } sub down_chain2string { return Bio::LiveSeq::Chain::down_chain2string(@_); } sub up_chain2string { return Bio::LiveSeq::Chain::up_chain2string(@_); } sub chain2string_verbose { croak "ambiguous method call. Explicit down_ or up_"; } sub down_chain2string_verbose { return Bio::LiveSeq::Chain::down_chain2string_verbose(@_); } sub up_chain2string_verbose { return Bio::LiveSeq::Chain::up_chain2string_verbose(@_); } sub invert_chain { return Bio::LiveSeq::Chain::invert_chain(@_); } sub mutate_element { croak "Old method name, please update code to: set_value_at_label"; } # new as of version 2.33 of Chain.pm sub down_labels { return Bio::LiveSeq::Chain::down_labels(@_); } sub up_labels { return Bio::LiveSeq::Chain::up_labels(@_); } sub start { return Bio::LiveSeq::Chain::start(@_); } sub end { return Bio::LiveSeq::Chain::end(@_); } sub label_exists { return Bio::LiveSeq::Chain::label_exists(@_); } sub get_value_at_pos { croak "ambiguous method call. Explicit down_ or up_"; } sub down_get_value_at_pos { return Bio::LiveSeq::Chain::down_get_value_at_pos(@_); } sub up_get_value_at_pos { return Bio::LiveSeq::Chain::up_get_value_at_pos(@_); } sub set_value_at_pos { croak "ambiguous method call. Explicit down_ or up_"; } sub down_set_value_at_pos { return Bio::LiveSeq::Chain::down_set_value_at_pos(@_); } sub up_set_value_at_pos { return Bio::LiveSeq::Chain::up_set_value_at_pos(@_); } sub get_value_at_label { return Bio::LiveSeq::Chain::get_value_at_label(@_); } sub set_value_at_label { return Bio::LiveSeq::Chain::set_value_at_label(@_); } sub get_label_at_pos { croak "ambiguous method call. Explicit down_ or up_"; } sub up_get_label_at_pos { return Bio::LiveSeq::Chain::up_get_label_at_pos(@_); } sub down_get_label_at_pos { return Bio::LiveSeq::Chain::down_get_label_at_pos(@_); } sub get_pos_of_label { croak "ambiguous method call. Explicit down_ or up_"; } sub up_get_pos_of_label { return Bio::LiveSeq::Chain::up_get_pos_of_label(@_); } sub down_get_pos_of_label { return Bio::LiveSeq::Chain::down_get_pos_of_label(@_); } # sub preinsert_string { return Bio::LiveSeq::Chain::praeinsert_string(@_); } sub preinsert_array { return Bio::LiveSeq::Chain::praeinsert_array(@_); } sub praeinsert_string { return Bio::LiveSeq::Chain::praeinsert_string(@_); } sub postinsert_string { return Bio::LiveSeq::Chain::postinsert_string(@_); } sub praeinsert_array { return Bio::LiveSeq::Chain::praeinsert_array(@_); } sub postinsert_array { return Bio::LiveSeq::Chain::postinsert_array(@_); } sub down_element{ return Bio::LiveSeq::Chain::down_element(@_); } sub up_element { return Bio::LiveSeq::Chain::up_element(@_); } sub is_downstream { return Bio::LiveSeq::Chain::is_downstream(@_); } sub is_upstream { return Bio::LiveSeq::Chain::is_upstream(@_); } sub check_chain { return Bio::LiveSeq::Chain::check_chain(@_); } sub chain_length { return Bio::LiveSeq::Chain::chain_length(@_); } sub splice_chain { return Bio::LiveSeq::Chain::splice_chain(@_); } sub pos_of_element { croak "ambiguous and old method name. use: down_pos_of_label"; } sub up_pos_of_element { croak "old method name. use: down_pos_of_label"; return Bio::LiveSeq::Chain::up_pos_of_element(@_); } sub down_pos_of_element { croak "old method name. use: up_pos_of_label"; return Bio::LiveSeq::Chain::down_pos_of_element(@_); } sub subchain_length { croak "ambiguous method call. Explicit down_ or up_"; } sub down_subchain_length { return Bio::LiveSeq::Chain::down_subchain_length(@_); } sub up_subchain_length { return Bio::LiveSeq::Chain::up_subchain_length(@_); } # these have to be deleted and changed names to conform to terminology sub elements { return Bio::LiveSeq::Chain::down_elements(@_); } sub up_elements { return Bio::LiveSeq::Chain::up_elements(@_); } sub down_elements { return Bio::LiveSeq::Chain::down_elements(@_); } 1;  File: pm.info, Node: Bio/LiveSeq/DNA, Next: Bio/LiveSeq/Exon, Prev: Bio/LiveSeq/ChainI, Up: Module List DNA object for LiveSeq ********************** NAME ==== Bio::LiveSeq::DNA - DNA object for LiveSeq SYNOPSIS ======== # documentation needed DESCRIPTION =========== This holds the DNA sequence (or the RNA in the case of cDNA entries) and is accessed by exons, genes, transcripts... objects AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net 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 _ new === Title : new Usage : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca", -offset => 3 ); Function: generates a new Bio::LiveSeq::DNA Returns : reference to a new object of class DNA Errorcode -1 Args : a string AND an optional offset to create nucleotide labels (default is 1, i.e. starting the count of labels from "1") -> do not bother using it -> it could be used by alternative loaders !EMBL format NOTE : strand of DNA is set to 1 by default  File: pm.info, Node: Bio/LiveSeq/Exon, Next: Bio/LiveSeq/Gene, Prev: Bio/LiveSeq/DNA, Up: Module List Range abstract class for LiveSeq ******************************** NAME ==== Bio::LiveSeq::Exon - Range abstract class for LiveSeq SYNOPSIS ======== # documentation needed DESCRIPTION =========== Class for EXON objects. They consist of a beginlabel, an endlabel (both referring to a LiveSeq DNA object) and a strand. The strand could be 1 (forward strand, default), -1 (reverse strand). AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net 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 _ new === Title : new Usage : $exon1 = Bio::LiveSeq::Exon-> new(-seq => $objref, -start => $startlabel, -end => $endlabel, -strand => 1); Function: generates a new Bio::LiveSeq::Exon Returns : reference to a new object of class Exon Errorcode -1 Args : two labels and an integer get_Transcript -------------- Title : get_Transcript Usage : $transcript = $obj->get_Transcript() Function: retrieves the reference to the object of class Transcript (if any) attached to a LiveSeq object Returns : object reference Args : none Note : only Exons that compose a Transcript (i.e. those created out of a CDS Entry-Feature) will have an attached Transcript  File: pm.info, Node: Bio/LiveSeq/Gene, Next: Bio/LiveSeq/IO/BioPerl, Prev: Bio/LiveSeq/Exon, Up: Module List Range abstract class for LiveSeq ******************************** NAME ==== Bio::LiveSeq::Gene - Range abstract class for LiveSeq SYNOPSIS ======== # documentation needed DESCRIPTION =========== This is used as storage for all object references concerning a particular gene. AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net 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 _ new === Title : new Usage : $gene = Bio::LiveSeq::Gene->new(-name => "name", -features => $hashref -upbound => $min -downbound => $max); Function: generates a new Bio::LiveSeq::Gene Returns : reference to a new object of class Gene Errorcode -1 Args : one string and one hashreference containing all features defined for the Gene and the references to the LiveSeq objects for those features. Two labels for defining boundaries of the gene. Usually the boundaries will reflect max span of transcript, exon... features, while the DNA sequence will be created with some flanking regions (e.g. with the EMBL_SRS::gene2liveseq routine). If these two labels are not given, they will default to the start and end of the DNA object. Note : the format of the hash has to be like DNA => reference to LiveSeq::DNA object Transcripts => reference to array of transcripts objrefs Transclations => reference to array of transcripts objrefs Exons => .... Introns => .... Prim_Transcripts => .... Repeat_Units => .... Repeat_Regions => .... Only DNA and Transcripts are mandatory