This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/Search/Processor/Fasta, Next: Bio/Search/Processor/ProcessorI, Prev: Bio/Search/Processor, Up: Module List Processor of Fasta-generated data streams ***************************************** NAME ==== Bio::Search::Processor::Fasta - Processor of Fasta-generated data streams SYNOPSIS ======== use Bio::Search::Processor my $processor = new Bio::Search::Processor -file => 'mysearchrun', -algorithm => 'Fasta'; DESCRIPTION =========== A Processor object is used to generate Bio::Search::Result::* objects, given a source of Search data (a file or filehandle). The Processor object works very much like the SeqIO system: once initialized with the new() method, the Processor object will continue to yield as many Result objects as are available from the data source (for single "runs" this is often only one Result object). 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 bioperl-guts-l@bioperl.org - Automated bug and CVS messages 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 ===================== Email amackey@virginia.edu Describe contact details here APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_result ----------- Title : next_result Usage : $result = $processor->next_result() Function: Used to obtain Result objects from a FASTA-generated data source Returns : a Bio::Search::Result::Fasta object Args :  File: pm.info, Node: Bio/Search/Processor/ProcessorI, Next: Bio/Search/Result/Fasta, Prev: Bio/Search/Processor/Fasta, Up: Module List Abstract Interface for Processor Objects **************************************** NAME ==== Bio::Search::Processor::ProcessorI - Abstract Interface for Processor Objects SYNOPSIS ======== use Bio::Search::Processor my $processor = new Bio::Search::Processor -file => 'mysearchrun', -algorithm => 'Blast'; while ($result = $processor->next_result()) { $id = $result->get_query_id(); $lib = $result->get_library_name(); $size = $result->get_library_size(); foreach $hit ( $result->get_hits() ) { $matchid = $hit->get_id(); $matchdesc = $hit->get_desc(); # etc, etc, do stuff. } } DESCRIPTION =========== A Processor object is used to generate Bio::Search::Result::* objects, given a source of Search data (a file or filehandle). The Processor object works very much like the SeqIO system: once initialized with the new() method, the Processor object will continue to yield as many Result objects as are available from the data source (for single "runs" this is often only one Result object). 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 bioperl-guts-l@bioperl.org - Automated bug and CVS messages 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 ===================== Email amackey@virginia.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_result ----------- Title : next_result Usage : $result = $processor->next_result() Function: Returns the next Bio::Search::Result::* object available from the provided data stream or undef if no more are available. Returns : Bio::Search::Result object Args :  File: pm.info, Node: Bio/Search/Result/Fasta, Next: Bio/Search/Result/ResultI, Prev: Bio/Search/Processor/ProcessorI, Up: Module List Result object for FASTA-generated data sources ********************************************** NAME ==== Bio::Search::Result::Fasta - Result object for FASTA-generated data sources SYNOPSIS ======== These objects are generated automatically by Bio::Search::Processor::Fasta, and shouldn't be used directly. DESCRIPTION =========== Bio::Search::Result::* objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::* 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 bioperl-guts-l@bioperl.org - Automated bug and CVS messages 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 ===================== Email amackey@virginia.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _  File: pm.info, Node: Bio/Search/Result/ResultI, Next: Bio/SearchDist, Prev: Bio/Search/Result/Fasta, Up: Module List Abstract interface to Result objects ************************************ NAME ==== Bio::Search::Result::ResultI.pm - Abstract interface to Result objects SYNOPSIS ======== These objects are generated automatically by Bio::Search::Processor objects, and wouldn't be used directly. DESCRIPTION =========== Bio::Search::Result::* objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few fundamental elements, including the ability to return Bio::Search::Hit::* 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 bioperl-guts-l@bioperl.org - Automated bug and CVS messages 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 ===================== Email amackey@virginia.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ get_query_id ------------ Title : get_query_id Usage : $id = $result->get_query_id(); Function: Used to obtain the string identifier of the query used by the algorithm. Returns : a scalar string. Args : get_library_name ---------------- Title : get_library_name Usage : $name = $result->get_library_name() Function: Used to obtain the name of the library that the query was searched against by the algorithm. Returns : a scalar string Args : get_library_size ---------------- Title : get_library_size Usage : $size = $result->get_library_size() Function: Used to obtain the size of library that was searched against. Returns : a scalar integer (units specific to algorithm, but probably the total number of residues in the library, if available) or undef if the information was not available to the Processor object. Args : get_library_count ----------------- Title : get_library_count Usage : $count = $result->get_library_count() Function: Used to obtain the number of entries contained in the library. Returns : a scalar integer representing the number of entities in the library or undef if the information was not available. Args : get_hits -------- Title : get_hits Usage : @hits = $result->get_hits(); Function: Used to obtain the array of hit objects, representing potential matches between the query and various entities from the library. Returns : an array of Bio::Search::Hit::* object (specific type depends on algorithm), or undef if there were none. Args :  File: pm.info, Node: Bio/SearchDist, Next: Bio/Seq, Prev: Bio/Search/Result/ResultI, Up: Module List A perl wrapper around Sean Eddy's histogram object ************************************************** NAME ==== Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object SYNOPSIS ======== $dis = Bio::SearchDist->new(); foreach $score ( @scores ) { $dis->add_score($score); } if( $dis->fit_evd() ) { foreach $score ( @scores ) { $evalue = $dis->evalue($score); print "Score $score had an evalue of $evalue\n"; } } else { warn("Could not fit histogram to an EVD!"); } DESCRIPTION =========== The Bio::SearchDist object is a wrapper around Sean Eddy's excellent histogram object. The histogram object can bascially take in a number of scores which are sensibly distributed somewhere around 0 that come from a supposed Extreme Value Distribution. Having add all the scores from a database search via the add_score method you can then fit a extreme value distribution using fit_evd(). Once fitted you can then get out the evalue for each score (or a new score) using evalue($score). The fitting procedure is better described in Sean Eddy's own code (available from http://hmmer.wustl.edu, or in the histogram.h header file in Compile/SW). Bascially it fits a EVD via a maximum likelhood method with pruning of the top end of the distribution so that real positives are discarded in the fitting procedure. This comes from an orginally idea of Richard Mott's and the likelhood fitting is from a book by Lawless [should ref here]. The object relies on the fact that the scores are sensibly distributed around about 0 and that integer bins are sensible for the histogram. Scores based on bits are often ideal for this (bits based scoring mechanisms is what this histogram object was originally designed for). CONTACT ======= The original code this was based on comes from the histogram module as part of the HMMer2 package. Look at http://hmmer.wustl.edu/ Its use in Bioperl is via the Compiled XS extension which is cared for by Ewan Birney (birney@sanger.ac.uk). Please contact Ewan first about the use of this module 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/ APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ add_score --------- Title : add_score Usage : $dis->add_score(300); Function: Adds a single score to the distribution Returns : nothing Args : fit_evd ------- Title : fit_evd Usage : $dis->fit_evd(); Function: fits an evd to the current distribution Returns : 1 if it fits successfully, 0 if not Args : fit_Gaussian ------------ Title : fit_Gaussian Usage : Function: Example : Returns : Args : evalue ------ Title : evalue Usage : $eval = $dis->evalue($score) Function: Returns the evalue of this score Returns : float Args : _engine ------- Title : _engine Usage : $obj->_engine($newval) Function: underlyine bp_sw:: histogram engine Returns : value of _engine Args : newvalue (optional)  File: pm.info, Node: Bio/Seq, Next: Bio/Seq/LargePrimarySeq, Prev: Bio/SearchDist, Up: Module List Sequence object, with features ****************************** NAME ==== Bio::Seq - Sequence object, with features SYNOPSIS ======== $seqio = Bio::SeqIO->new ( '-format' => 'embl' , -file => 'myfile.dat'); $seqobj = $seqio->next_seq(); # features must implement Bio::SeqFeatureI @features = $seqobj->top_SeqFeatures(); # just top level @features = $seqobj->all_SeqFeatures(); # descend into sub features $seq = $seqobj->seq(); # actual sequence as a string $seqstr = $seqobj->subseq(10,50); $ann = $seqobj->annotation(); # annotation object DESCRIPTION =========== A Seq object is a sequence with sequence features placed on them. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In bioperl we have 3 main players that people are going to use Bio::PrimarySeq - just the sequence and its names, nothing else. Bio::SeqFeatureI - a location on a sequence, potentially with a sequence. and annotation Bio::Seq - A sequence and a collection of seqfeatures (an aggregate) with its own annotation. Although bioperl is not tied to file formats heavily, these distinctions do map to file formats sensibly and for some bioinformaticians this might help you: Bio::PrimarySeq - Fasta file of a sequence Bio::SeqFeatureI - A single entry in an EMBL/GenBank/DDBJ feature table Bio::Seq - A single EMBL/GenBank/DDBJ entry By having this split we avoid alot of nasty ciricular references (seqfeatures can hold a reference to a sequence without the sequence holding a reference to the seqfeature). Ian Korf really helped in the design of the Seq and SeqFeature system. 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@bioperl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney, inspired by Ian Korf objects ================================================== Email birney@sanger.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 _ new --- Title : new Usage : $seq = Bio::Seq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new seq object from basic constructors, being a string for the sequence and strings for id and accession_number Returns : a new Bio::Seq object PrimarySeq interface ==================== The primaryseq interface is the basic sequence getting and setting methods found on all sequences. These methods implement the PrimarySeq interface by delegating to the primary_seq inside the object. This means that you can use a Seq object wherever there is a PrimarySeq, and of course, you are free to use these functions anyway. seq --- Title : seq Usage : $string = $obj->seq() Function: Returns the sequence as a string of letters. The case of the letters is left up to the implementer. Suggested cases are upper case for proteins and lower case for DNA sequence (IUPAC standard), but implementations are suggested to keep an open mind about case (some users... want mixed case!) Returns : A scalar length ------ Title : length Usage : $len = $seq->length() Function: Example : Returns : integer representing the length of the sequence. Args : subseq ------ Title : subseq Usage : $substring = $obj->subseq(10,40); Function: returns the subseq from start to end, where the first base is 1 and the number is inclusive, ie 1-2 are the first two bases of the sequence Start cannot be larger than end but can be equal Returns : a string Args : display_id ---------- Title : display_id Usage : $id_string = $obj->display_id($newid); Function: returns or sets the display id, aka the common name of the Sequence object. The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the ID field of the GenBank/EMBL databanks and the id field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this. Notice that $seq->id() maps to this function, mainly for legacy/convience issues Returns : A string Args : newid (optional) accession_number ---------------- Title : accession_number Usage : $unique_biological_key = $obj->accession_number; Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implemetation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string Args : None desc ---- Title : desc Usage : $seqobj->desc() Function: Sets/Gets the description of the sequnce Example : Returns : Args : primary_id ---------- Title : primary_id Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a way the implementaiton can control clients can expect one id to map to one object. For sequences with no natural id, this method should return a stringified memory location. Also notice that this method is B delegated to the internal PrimarySeq object Returns : A string Args : None can_call_new ------------ Title : can_call_new Usage : if( $obj->can_call_new ) { $newobj = $obj->new( %param ); } Function: can_call_new returns 1 or 0 depending on whether an implementation allows new constructor to be called. If a new constructor is allowed, then it should take the followed hashed constructor list. $myobject->new( -seq => $sequence_as_string, -display_id => $id -accession_number => $accession -moltype => 'dna', ); Example : Returns : 1 or 0 Args : moltype ------- Title : moltype Usage : if( $obj->moltype eq 'dna' ) { /Do Something/ } Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive. This is not called because this would cause upgrade problems from the 0.5 and earlier Seq objects. Returns : a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess. Args : none Methods provided in the Bio::PrimarySeqI interface ================================================== These methods are inherited from the PrimarySeq interface and work as one expects, building new Bio::Seq objects or other information as expected. Sequence Features are not transfered to the new objects. This is possibly a mistake. Anyone who feels the urge in dealing with this is welcome to give it a go. revcom ------ Title : revcom Usage : $rev = $seq->revcom() Function: Produces a new Bio::Seq object which is the reversed complement of the sequence. For protein sequences this throws an exception of "Sequence is a protein. Cannot revcom" The id is the same id as the orginal sequence, and the accession number is also indentical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions To do an inplace edit of an object you can go: $seq = $seq->revcom(); This of course, causes Perl to handle the garbage collection of the old object, but it is roughly speaking as efficient as an inplace edit. Returns : A new (fresh) Bio::Seq object Args : none trunc ----- Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::Seq object Args : id -- Title : id Usage : $id = $seq->id() Function: This is mapped on display_id Example : Returns : Args : Seq only methods ================ These methods are specific to the Bio::Seq object, and not found on the Bio::PrimarySeq object primary_seq ----------- Title : primary_seq Usage : $obj->primary_seq($newval) Function: Example : Returns : value of primary_seq Args : newvalue (optional) annotation ---------- Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional) add_SeqFeature -------------- Title : add_SeqFeature Usage : $seq->add_SeqFeature($feat); $seq->add_SeqFeature(@feat); Function: Adds the given feature object (or each of an array of feature objects to the feature array of this sequence. The object passed is required to implement the Bio::SeqFeatureI interface. Example : Returns : TRUE on success Args : A Bio::SeqFeatureI implementing object, or an array of such objects. top_SeqFeatures --------------- Title : top_SeqFeatures Usage : @feat_ary = $seq->top_SeqFeatures(); Function: Returns the array of top-level features for this sequence object. Features which are not top-level are subfeatures of one or more of the returned feature objects, which means that you must traverse the subfeature arrays of each top-level feature object in order to traverse all features associated with this sequence. Use all_SeqFeatures() if you want the feature tree flattened into one single array. Example : Returns : An array of Bio::SeqFeatureI implementing objects. Args : all_SeqFeatures --------------- Title : all_SeqFeatures Usage : @feat_ary = $seq->all_SeqFeatures(); Function: Returns the tree of feature objects attached to this sequence object flattened into one single array. Top-level features will still contain their subfeature-arrays, which means that you will encounter subfeatures twice if you traverse the subfeature tree of the returned objects. Use top_SeqFeatures() if you want the array to contain only the top-level features. Example : Returns : An array of Bio::SeqFeatureI implementing objects. Args : feature_count ------------- Title : feature_count Usage : $seq->feature_count() Function: Return the number of SeqFeatures attached to a sequence Example : Returns : number of SeqFeatures Args : none species ------- Title : species Usage : Function: Gets or sets the species Example : $species = $self->species(); Returns : Bio::Species object Args : Bio::Species object or none;  File: pm.info, Node: Bio/Seq/LargePrimarySeq, Next: Bio/Seq/LargeSeq, Prev: Bio/Seq, Up: Module List PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::RootI ********************************************************************************************************************************* NAME ==== Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::RootI SYNOPSIS ======== # normal primary seq usage DESCRIPTION =========== This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq otherwise the entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq->subseq(10,100) will cause only 90 characters to be brought into real memory. 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 - Ewan Birney, Jason Stajich =================================== Email birney@ebi.ac.uk 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 _ seq --- Title : seq Usage : Function: Example : Returns : Args : subseq ------ Title : subseq Usage : Function: Example : Returns : Args : add_sequence_as_string ---------------------- Title : add_sequence_as_string Usage : Function: Example : Returns : Args : _filename --------- Title : _filename Usage : $obj->_filename($newval) Function: Example : Returns : value of _filename Args : newvalue (optional)  File: pm.info, Node: Bio/Seq/LargeSeq, Next: Bio/Seq/RichSeq, Prev: Bio/Seq/LargePrimarySeq, Up: Module List SeqI compliant object that stores sequence as files in /tmp *********************************************************** NAME ==== Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp SYNOPSIS ======== # normal primary seq usage DESCRIPTION =========== This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!). Of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq otherwise the entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq->subseq(10,100) will cause only 90 characters to be brought into real memory. 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://www.bioperl.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 APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ trunc ----- Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::SeqI object Args :  File: pm.info, Node: Bio/Seq/RichSeq, Next: Bio/Seq/RichSeqI, Prev: Bio/Seq/LargeSeq, Up: Module List Module implementing a sequence created from a rich sequence database entry ************************************************************************** NAME ==== Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry SYNOPSIS ======== See Bio::Seq::RichSeqI and documentation of methods. DESCRIPTION =========== This module implements Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided. 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 - 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 _ new --- Title : new Usage : $seq = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', ); Function: Returns a new seq object from basic constructors, being a string for the sequence and strings for id and accession_number Returns : a new Bio::Seq::RichSeq object division -------- Title : division Usage : $obj->division($newval) Function: Returns : value of division Args : newvalue (optional) molecule -------- Title : molecule Usage : $obj->molecule($newval) Function: Returns : type of molecule (DNA, mRNA) Args : newvalue (optional) add_date -------- Title : add_date Usage : $self->add_date($datestr) Function: adds a date Example : Returns : a date string or an array of such strings Args : get_dates --------- Title : get_dates Usage : Function: Example : Returns : an array of date strings Args : pid --- Title : pid Usage : Function: Get (and set, depending on the implementation) the PID property for the sequence. Example : Returns : a string Args : accession --------- Title : accession Usage : $obj->accession($newval) Function: Whilst the underlying sequence object does not have an accession, so we need one here. In this implementation this is merely a synonym for accession_number(). Example : Returns : value of accession Args : newvalue (optional) add_secondary_accession ----------------------- Title : add_secondary_accession Usage : $self->add_domment($ref) Function: adds a secondary_accession Example : Returns : Args : a string or an array of strings get_secondary_accessions ------------------------ Title : get_secondary_accessions Usage : Function: Example : Returns : An array of strings Args : seq_version ----------- Title : seq_version Usage : $obj->seq_version($newval) Function: Example : Returns : value of seq_version Args : newvalue (optional) keywords -------- Title : keywords Usage : $obj->keywords($newval) Function: Returns : value of keywords (a string) Args : newvalue (optional) (a string)  File: pm.info, Node: Bio/Seq/RichSeqI, Next: Bio/SeqAnalysisParserI, Prev: Bio/Seq/RichSeq, Up: Module List RichSeq interface, mainly for database orientated sequences *********************************************************** NAME ==== Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences SYNOPSIS ======== @secondary = $richseq->get_secondary_accessions; $division = $richseq->division; $mol = $richseq->molecule; @dates = $richseq->get_dates; $seq_version = $richseq->seq_version; $pid = $richseq->pid; DESCRIPTION =========== This interface extends the Bio::SeqI interface to give additional functionality to sequences with richer data sources, in particular from database sequences (EMBL, GenBank and Swissprot). 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 - 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 _ get_secondary_accessions ------------------------ Title : get_secondary_accessions Usage : Function: Get the secondary accessions for a sequence. Example : Returns : an array of strings Args : none division -------- Title : division Usage : Function: Get (and set, depending on the implementation) the divison for a sequence. Examples from GenBank are PLN (plants), PRI (primates), etc. Example : Returns : a string Args : molecule -------- Title : molecule Usage : Function: Get (and set, depending on the implementation) the molecule type for the sequence. This is not necessarily the same as Bio::PrimarySeqI::moltype(), because it is databank-specific. Example : Returns : a string Args : pid --- Title : pid Usage : Function: Get (and set, depending on the implementation) the PID property for the sequence. Example : Returns : a string Args : get_dates --------- Title : get_dates Usage : Function: Get (and set, depending on the implementation) the dates the databank entry specified for the sequence Example : Returns : an array of strings Args : seq_version ----------- Title : seq_version Usage : Function: Get (and set, depending on the implementation) the version string of the sequence. Example : Returns : a string Args :  File: pm.info, Node: Bio/SeqAnalysisParserI, Next: Bio/SeqFeature/FeaturePair, Prev: Bio/Seq/RichSeqI, Up: Module List Sequence analysis output parser interface ***************************************** NAME ==== Bio::SeqAnalysisParserI - Sequence analysis output parser interface SYNOPSIS ======== # get a SeqAnalysisParserI somehow, e.g. by my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser( '-input' => 'inputfile', '-method' => 'genscan'); while( my $feature = $parser->next_feature() ) { print "Feature from ", $feature->start, " to ", $feature->end, "\n"; } DESCRIPTION =========== SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. Sequence analysis in this sense is a search for similarities or the identification of features on the sequence, like a databank search or a a gene prediction result. The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used e.g. in high-throughput automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers without the necessity for modifying the core of the annotation pipeline. In this concept the annotation pipeline has to rely on only a list of methods for which to process the results, and a factory from which it can obtain the corresponding parser implementing this interface. See Bio::Factory::SeqAnalysisParserFactoryI and Bio::Factory::SeqAnalysisParserFactory for interface and an implementation of the corresponding factory. 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 _ new --- Title : new Remark : Classes implementing this interface are expected to implement recognition of at least the following named parameters: -file input file (alternative to -fh) -fh input stream (alternative to -file) next_feature ------------ Title : next_feature Usage : $seqfeature = $obj->next_feature(); Function: Returns the next feature available in the analysis result, or undef if there are no more features. Example : Returns : A Bio::SeqFeatureI implementing object, or undef if there are no more features. Args : none  File: pm.info, Node: Bio/SeqFeature/FeaturePair, Next: Bio/SeqFeature/Gene/Exon, Prev: Bio/SeqAnalysisParserI, Up: Module List hold pair feature information e.g. blast hits ********************************************* NAME ==== Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits SYNOPSIS ======== my $feat = new Bio::SeqFeature::FeaturePair(-feature1 => $f1, -feature2 => $f2, ); # Bio::SeqFeatureI methods can be used my $start = $feat->start; my $end = $feat->end; # Bio::FeaturePair methods can be used my $hstart = $feat->hstart; my $hend = $feat->hend; my $feature1 = $feat->feature1; # returns feature1 object DESCRIPTION =========== A sequence feature object where the feature is itself a feature on another sequence - e.g. a blast hit where residues 1-40 of a protein sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence HS120G22. The genomic sequence coordinates are used to create one sequence feature $f1 and the protein coordinates are used to create feature $f2. A FeaturePair object can then be made my $fp = new Bio::SeqFeature::FeaturePair(-feature1 => $f1, # genomic -feature2 => $f2, # protein ); This object can be used as a standard Bio::SeqFeatureI in which case my $gstart = $fp->start # returns start coord on feature1 - genomic seq. my $gend = $fp->end # returns end coord on feature1. In general standard Bio::SeqFeatureI method calls return information in feature1. Data in the feature 2 object are generally obtained using the standard methods prefixed by h (for hit!) my $pstart = $fp->hstart # returns start coord on feature2 = protein seq. my $pend = $fp->hend # returns end coord on feature2. If you wish to swap feature1 and feature2 around : $feat->invert so... $feat->start # etc. returns data in $feature2 object No sub_SeqFeatures or tags can be stored in this object directly. Any features or tags are expected to be stored in the contained objects feature1, and feature2. CONTACT ======= Ewan Birney APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ feature1 -------- Title : feature1 Usage : $f = $featpair->feature1 $featpair->feature1($feature) Function: Get/set for the query feature Returns : Bio::SeqFeatureI Args : Bio::SeqFeatureI feature2 -------- Title : feature2 Usage : $f = $featpair->feature2 $featpair->feature2($feature) Function: Get/set for the hit feature Returns : Bio::SeqFeatureI Args : Bio::SeqFeatureI start ----- Title : start Usage : $start = $featpair->start $featpair->start(20) Function: Get/set on the start coordinate of feature1 Returns : integer Args : [optional] beginning of feature end --- Title : end Usage : $end = $featpair->end $featpair->end($end) Function: get/set on the end coordinate of feature1 Returns : integer Args : [optional] ending point of feature strand ------ Title : strand Usage : $strand = $feat->strand() $feat->strand($strand) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : [optional] strand information to set location -------- Title : location Usage : $location = $featpair->location $featpair->location($location) Function: Get/set location object (using feature1) Returns : Bio::LocationI object Args : [optional] LocationI to store score ----- Title : score Usage : $score = $feat->score() $feat->score($score) Function: get/set on score information Returns : float Args : none if get, the new value if set frame ----- Title : frame Usage : $frame = $feat->frame() $feat->frame($frame) Function: get/set on frame information Returns : 0,1,2 Args : none if get, the new value if set primary_tag ----------- Title : primary_tag Usage : $ptag = $featpair->primary_tag Function: get/set on the primary_tag of feature1 Returns : 0,1,2 Args : none if get, the new value if set source_tag ---------- Title : source_tag Usage : $tag = $feat->source_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none seqname ------- Title : seqname Usage : $obj->seqname($newval) Function: There are many cases when you make a feature that you do know the sequence name, but do not know its actual sequence. This is an attribute such that you can store the seqname. This attribute should *not* be used in GFF dumping, as that should come from the collection in which the seq feature was found. Returns : value of seqname Args : newvalue (optional) hseqname -------- Title : hseqname Usage : $featpair->hseqname($newval) Function: Get/set method for the name of feature2. Returns : value of $feature2->seqname Args : newvalue (optional) hstart ------ Title : hstart Usage : $start = $featpair->hstart $featpair->hstart(20) Function: Get/set on the start coordinate of feature2 Returns : integer Args : none hend ---- Title : hend Usage : $end = $featpair->hend $featpair->hend($end) Function: get/set on the end coordinate of feature2 Returns : integer Args : none hstrand ------- Title : hstrand Usage : $strand = $feat->strand() $feat->strand($strand) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : none hscore ------ Title : hscore Usage : $score = $feat->score() $feat->score($score) Function: get/set on score information Returns : float Args : none if get, the new value if set hframe ------ Title : hframe Usage : $frame = $feat->frame() $feat->frame($frame) Function: get/set on frame information Returns : 0,1,2 Args : none if get, the new value if set hprimary_tag ------------ Title : hprimary_tag Usage : $ptag = $featpair->hprimary_tag Function: Get/set on the primary_tag of feature2 Returns : 0,1,2 Args : none if get, the new value if set hsource_tag ----------- Title : hsource_tag Usage : $tag = $feat->hsource_tag() $feat->source_tag('genscan'); Function: Returns the source tag for a feature, eg, 'genscan' Returns : a string Args : none invert ------ Title : invert Usage : $tag = $feat->invert Function: Swaps feature1 and feature2 around Returns : Nothing Args : none  File: pm.info, Node: Bio/SeqFeature/Gene/Exon, Next: Bio/SeqFeature/Gene/ExonI, Prev: Bio/SeqFeature/FeaturePair, Up: Module List a feature representing an exon ****************************** NAME ==== Bio::SeqFeature::Gene::Exon - a feature representing an exon SYNOPSIS ======== # obtain an exon instance $exon somehow print "exon from ", $exon->start(), " to ", $exon->end(), " on seq ", $exon->seqname(), ", strand ", $exon->strand(), ", encodes the peptide sequence ", $exon->cds()->translate()->seq(), "\n"; DESCRIPTION =========== This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic. FEEDBACK ======== Mailing Lists ------------- User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp ==================== Email hlapp@gmx.net Describe contact details here APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ is_coding --------- Title : is_coding Usage : if($exon->is_coding()) { # do something } if($is_utr) { $exon->is_coding(0); } Function: Get/set whether or not the exon codes for amino acid. Returns : TRUE if the object represents a feature translated into protein, and FALSE otherwise. Args : A boolean value on set. primary_tag ----------- Title : primary_tag Usage : $tag = $feat->primary_tag() $feat->primary_tag('exon') Function: Get/set the primary tag for the exon feature. This method is overridden here in order to allow only for tag values following a certain convention. For consistency reasons, the tag value must either contain the string 'exon' or the string 'utr' (both case-insensitive). In the case of 'exon', a string describing the type of exon may be appended or prefixed. Presently, the following types are allowed: initial, internal, and terminal (all case-insensitive). If the supplied tag value matches 'utr' (case-insensitive), is_coding() will automatically be set to FALSE, and to TRUE otherwise. Returns : A string. Args : A string on set. location -------- Title : location Usage : my $location = $exon->location() Function: Returns a location object suitable for identifying the location of the exon on the sequence or parent feature. This method is overridden here to restrict allowed location types to non-compound locations. Returns : Bio::LocationI object Args : none cds --- Title : cds() Usage : $cds = $exon->cds(); Function: Get the coding sequence of the exon as a sequence object. The sequence of the returned object is prefixed by Ns (lower case) if the frame of the exon is defined and different from zero. The result is that the first base starts a codon (frame 0). This implementation returns undef if the particular exon is not translated to protein, i.e., is_coding() returns FALSE. Undef will also be returned if no sequence is attached to this exon feature. Returns : A Bio::PrimarySeqI implementing object. Args :