This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/SeqIO/largefasta, Next: Bio/SeqIO/pir, Prev: Bio/SeqIO/genbank, Up: Module List method i/o on very large fasta sequence files ********************************************* NAME ==== Bio::SeqIO::largefasta - method i/o on very large fasta sequence files SYNOPSIS ======== Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION =========== This object can transform Bio::Seq objects to and from fasta flat file databases. This module handles very large sequence files by using the *Note Bio/Seq/LargePrimarySeq: Bio/Seq/LargePrimarySeq, module to store all the sequence data in a file. This can be a problem if you have limited disk space on your computer because this will effectively cause 2 copies of the sequence file to reside on disk for the life of the *Note Bio/Seq/LargePrimarySeq: Bio/Seq/LargePrimarySeq, object. The default location for this is specified by the *Note File/Spec: File/Spec,->tmpdir routine which is usually /tmp on UNIX. If a sequence file is larger than the swap space (capacity of the /tmp dir) this could cause problems for the machine. It is possible to set the directory where the temporary file is located by adding the following line to your code BEFORE calling next_seq. $Bio::Seq::LargePrimarySeq::DEFAULT_TEMP_DIR = 'newdir'; 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/ AUTHORS - Jason Stajich ======================= Email: jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq -------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE next_primary_seq ---------------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::PrimarySeq object Args : NONE write_seq --------- Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object  File: pm.info, Node: Bio/SeqIO/pir, Next: Bio/SeqIO/raw, Prev: Bio/SeqIO/largefasta, Up: Module List PIR sequence input/output stream ******************************** NAME ==== Bio::SeqIO::pir - PIR sequence input/output stream SYNOPSIS ======== Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION =========== This object can transform Bio::Seq objects to and from fasta flat file databases. 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.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/ AUTHORS ======= Aaron Mackey Lincoln Stein APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq -------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : write_seq --------- Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object  File: pm.info, Node: Bio/SeqIO/raw, Next: Bio/SeqIO/scf, Prev: Bio/SeqIO/pir, Up: Module List raw sequence file input/output stream ************************************* NAME ==== Bio::SeqIO::raw - raw sequence file input/output stream SYNOPSIS ======== Do not use this module directly. Use it via the *Note Bio/SeqIO: Bio/SeqIO, class. DESCRIPTION =========== This object can transform Bio::Seq objects to and from raw flat file databases. 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.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/ AUTHORS ======= Ewan Birney Lincoln Stein APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq -------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : write_seq --------- Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object  File: pm.info, Node: Bio/SeqIO/scf, Next: Bio/SeqIO/swiss, Prev: Bio/SeqIO/raw, Up: Module List SCF sequence input/output stream ******************************** NAME ==== Bio::SeqIO::scf - SCF sequence input/output stream SYNOPSIS ======== Do not use this module directly. Use it via the *Note Bio/SeqIO: Bio/SeqIO, class. DESCRIPTION =========== This object can transform Bio::Seq objects to and from SCF trace files. 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.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/ AUTHORS ======= Aaron Mackey Lincoln Stein lstein@cshl.org APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq -------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : write_seq --------- Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object  File: pm.info, Node: Bio/SeqIO/swiss, Next: Bio/SeqUtils, Prev: Bio/SeqIO/scf, Up: Module List Swissprot sequence input/output stream ************************************** NAME ==== Bio::SeqIO::swiss - Swissprot sequence input/output stream SYNOPSIS ======== It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'swiss'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } DESCRIPTION =========== This object can transform Bio::Seq objects to and from swissprot flat file databases. There is alot of flexibility here about how to dump things which I need to document fully. Optional functions ------------------ _show_dna() (output only) shows the dna or not _post_sort() (output only) provides a sorting func which is applied to the FTHelpers before printing _id_generation_func() This is function which is called as print "ID ", $func($seq), "\n"; To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools. =back 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 - Elia Stupka ==================== Email elia@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 _ next_seq -------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : write_seq --------- Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : Bio::Seq _generateCRCTable ----------------- Title : _generateCRCTable Usage : Function: Example : Returns : Args : _crc32 ------ Title : _crc32 Usage : Function: Example : Returns : Args : _print_swissprot_FTHelper ------------------------- Title : _print_swissprot_FTHelper Usage : Function: Example : Returns : Args : _read_swissprot_References -------------------------- Title : _read_swissprot_References Usage : Function: Reads references from swissprot format. Internal function really Example : Returns : Args : _read_swissprot_Species ----------------------- Title : _read_swissprot_Species Usage : Function: Reads the swissprot Organism species and classification lines. Example : Returns : A Bio::Species object Args : _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) _read_FTHelper_swissprot ------------------------ Title : _read_FTHelper_swissprot Usage : _read_FTHelper_swissprot(\$buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar _write_line_swissprot --------------------- Title : _write_line_swissprot Usage : Function: internal function Example : Returns : Args : _write_line_swissprot_regex --------------------------- Title : _write_line_swissprot_regex Usage : Function: internal function for writing lines of specified length, with different first and the next line left hand headers and split at specific points in the text Example : Returns : nothing Args : file handle, first header, second header, text-line, regex for line breaks, total line length _post_sort ---------- Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional) _show_dna --------- Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional) _id_generation_func ------------------- Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional) _ac_generation_func ------------------- Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional) _sv_generation_func ------------------- Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional) _kw_generation_func ------------------- Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional)  File: pm.info, Node: Bio/SeqUtils, Next: Bio/SimpleAlign, Prev: Bio/SeqIO/swiss, Up: Module List Additional methods for PrimarySeq objects ***************************************** NAME ==== Bio::SeqUtils - Additional methods for PrimarySeq objects SYNOPSIS ======== # get a Bio::PrimarySeqI compliant object, $seq, somehow $util = new Bio::SeqUtils; $poplypeptide_3char = $util->seq3($seq); #or $poplypeptide_3char = Bio::SeqUtils->seq3($seq); #set the sequence string (stored in one char code in the object) Bio::SeqUtils->seq3($seq, $poplypeptide_3char); DESCRIPTION =========== This class is a holder of methods that work on *Note Bio/PrimarySeqI: Bio/PrimarySeqI, compliant sequence objects, e.g. *Note Bio/PrimarySeq: Bio/PrimarySeq, and *Note Bio/Seq: Bio/Seq,. These methods are not part of the *Note Bio/PrimarySeqI: Bio/PrimarySeqI, interface and should in general not essential to the primary function of sequence objects. If you are thinking of adding essential functions, it might be better to create your own sequence class. The methods take as their first argument a sequence object. It is possible to use methods without first creating a SeqUtils object, i.e. use it as an anonymous hash. The first two methodsgive out or read in protein sequences coded in three letter IUPAC amino acid codes. 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 - Heikki Lehvaslaiho =========================== Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ seq3 ---- Title : seq3 Usage : $string = Bio::SeqUtils->seq3($seq) Function: Read only method that returns the amino acid sequence as a string of three letter codes. moltype has to be 'protein'. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa'. A noncoded aminoacid selenocystein is recognized (Sel, U). Returns : A scalar Args : character used for stop in the protein seqence optional, defaults to '*' string used to separate the output amino acid codes, optional, defaults to '' seq3in ------ Title : seq3in Usage : $string = Bio::SeqUtils->seq3in($seq, 'MetGlyTer') Function: Read only method that returns the amino acid sequence as a string of three letter codes. moltype has to be 'protein'. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa' Returns : Bio::PrimarySeq object; Args : character to be used for stop in the protein seqence, optional, defaults to '*' character to be used for unknown in the protein seqence, optional, defaults to 'X' string used to separate the output amino acid codes, optional, defaults to ''  File: pm.info, Node: Bio/SimpleAlign, Next: Bio/Species, Prev: Bio/SeqUtils, Up: Module List Multiple alignments held as a set of sequences ********************************************** NAME ==== SimpleAlign - Multiple alignments held as a set of sequences SYNOPSIS ======== $aln = new Bio::SimpleAlign; $aln->read_MSF(\*STDIN); $aln->write_fasta(\*STDOUT); INSTALLATION ============ This module is included with the central Bioperl distribution: http://bio.perl.org/Core/Latest ftp://bio.perl.org/pub/DIST Follow the installation instructions included in the README file. DESCRIPTION =========== SimpleAlign handles multiple alignments of sequences. It is very permissive of types (it wont insist on things being all same length etc): really it is a SequenceSet explicitly held in memory with a whole series of built in manipulations and especially file format systems for read/writing alignments. SimpleAlign basically views an alignment as an immutable block of text. SimpleAlign *is not* the object to be using if you want to perform complex alignment alignment manipulations. These functions are much better done by UnivAln by Georg Fuellen. However for lightweight display/formatting and minimal manipulation (e.g. removiung all-gaps columns) - this is the one to use. Tricky concepts. SimpleAlign expects name,start,end to be 'unique' in the alignment, and this is the key for the internal hashes. (name,start,end is abreviated nse in the code). However, in many cases people don't want the name/start-end to be displayed: either multiple names in an alignment or names specific to the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called 'displayname', and generally is what is used to print out the alignment. They default to name/start-end The SimpleAlign Module came from Ewan Birney's Align module PROGRESS ======== SimpleAlign is being slowly converted to bioperl coding standards, mainly by Ewan. Use Bio::Root::Object - done Use proper exceptions - done Use hashed constructor - not done! 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, birney@sanger.ac.uk SEE ALSO ======== Bio::LocatableSeq.pm http://bio.perl.org/Projects/modules.html - Online module documentation http://bio.perl.org/Projects/SeqAlign/ - Bioperl sequence alignment project http://bio.perl.org/ - Bioperl Project Homepage APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ addSeq ------ Title : addSeq Usage : $myalign->addSeq($newseq); : : Function : Adds another sequence to the alignment : *does not* align it - just adds it to the : hashes : Returns : nothing Argument : column_from_residue_number -------------------------- Title : column_from_residue_number Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence with the given name. For example, for the alignment Seq1/91-97 AC..DEF.GH Seq2/24-30 ACGG.RTY.. Seq3/43-51 AC.DDEFGHI column_from_residue_number( "Seq1", 94 ) returns 5. column_from_residue_number( "Seq2", 25 ) returns 2. column_from_residue_number( "Seq3", 50 ) returns 9. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Returns : A column number for the postion in the alignment of the given residue in the given sequence (1 = first column) Args : A sequence name (not a name/start-end) A residue number in the whole sequence (not just that segment of it in the alignment) consensus_string ---------------- Title : consensus_string Usage : $str = $ali->consensus_string($threshold_percent) Function : Makes a consensus Returns : Argument : Optional treshold ranging from 0 to 100. If consensus residue appears in fewer than threshold % of the sequences at a given location consensus_string will return a "?" at that location rather than the consensus letter. (Default value = 0%) consensus_aa ------------ Title : consensus_aa Usage : $consensus_residue = $ali->consensus_aa($residue_number, $threshold_percent) Function : Makes a consensus Returns : Argument : Optional treshold ranging from 0 to 100. If consensus residue appears in fewer than threshold % of the sequences at the specified location consensus_string will return a "?" rather than the consensus letter. (Default value = 0%) each_alphabetically ------------------- Title : each_alphabetically Usage : foreach $seq ( $ali->each_alphabetically() ) : : Function : returns an array of sequence object sorted : alphabetically by name and then by start point : : Does not change the order of the alignment Returns : Argument : eachSeq ------- Title : eachSeq Usage : foreach $seq ( $align->eachSeq() ) : : Function : gets an array of Seq objects from the : alignment : : Returns : an array Argument : nothing eachSeqWithId ------------- Title : eachSeqWithId Usage : foreach $seq ( $align->eachSeqWithName() ) : : Function : gets an array of Seq objects from the : alignment, the contents being those sequences : with the given name (there may be more than one : Returns : an array Argument : nothing id -- Title : id Usage : $myalign->id("Ig") Function : Gets/sets the id field of the alignment : Returns : An id string Argument : An id string (optional) is_flush -------- Title : is_flush Usage : if( $ali->is_flush() ) : : Function : Tells you whether the alignment : is flush, ie all of the same length : : Returns : 1 or 0 Argument : length_aln ---------- Title : length_aln() Usage : $len = $ali->length_aln() : : Function : returns the maximum length of the alignment. : To be sure the alignment is a block, use is_flush : : Returns : Argument : map_chars --------- Title : map_chars Usage : $ali->map_chars('\.','-') : : Function : does a s/$arg1/$arg2/ on : the sequences. Useful for : gap characters : : Notice that the from (arg1) is interpretted : as a regex, so be careful about quoting meta : characters (eg $ali->map_chars('.','-') wont : do what you want) Returns : Argument : no_residues ----------- Title : no_residues Usage : $no = $ali->no_residues : : Function : number of residues in total : in the alignment : : Returns : Argument : no_sequences ------------ Title : no_sequences Usage : $depth = $ali->no_sequences : : Function : number of sequence in the : sequence alignment : : Returns : Argument : percentage_identity ------------------- Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function uses a fast method to calculate the average percentage identity of the alignment Returns : The average percentage identity of the alignment Args : None purge ----- Title : purge Usage : $aln->purge(0.7); Function: removes sequences above whatever %id Example : Returns : An array of the removed sequences Arguments This function will grind on large alignments. Beware! (perhaps not ideally implemented) read_fasta ---------- Title : read_fasta Usage : $ali->read_fasta(\*INPUT) : : Function : reads in a fasta formatted : file for an alignment : : Returns : Argument : read_mase --------- Title : read_mase Usage : $ali->read_mase(\*INPUT) : : Function : reads mase (seaview) : formatted alignments : : Returns : Argument : read_MSF -------- Title : read_MSF Usage : $al->read_MSF(\*STDIN); Function: reads MSF formatted files. Tries to read *all* MSF It reads all non whitespace characters in the alignment area. For MSFs with weird gaps (eg ~~~) map them by using $al->map_chars('~','-'); Example : Returns : Args : filehandle read_Pfam --------- Title : read_Pfam Usage : $ali->read_Pfam(\*INPUT) : : Function : reads a Pfam formatted : Alignment (Mul format). : - this is the format used by Belvu : Returns : Argument : read_Pfam_file -------------- Title : read_Pfam_file Usage : $ali->read_Pfam_file("thisfile"); : Function : opens a filename, reads : a Pfam (mul) formatted alignment : : : Returns : Argument : read_Prodom ----------- Title : read_Prodom Usage : $ali->read_Prodom( $file ) Function: Reads in a Prodom format alignment Returns : Args : A filehandle glob or ref. to a filehandle object read_selex ---------- Title : read_selex Usage : $ali->read_selex(\*INPUT) : : Function : reads selex (hmmer) format : alignments : : Returns : Argument : read_stockholm -------------- Title : read_stockholm Usage : $ali->read_stockholm(\*INPUT) : : Function : reads stockholm format alignments : : Returns : Argument : removeSeq --------- Title : removeSeq Usage : $aln->removeSeq($seq); Function : removes a single sequence from an alignment set_displayname_count --------------------- Title : set_displayname_count Usage : $ali->set_displayname_count : : Function : sets the names to be name_# : where # is the number of times this : name has been used. : Returns : Argument : set_displayname_flat -------------------- Title : set_displayname_flat Usage : $ali->set_displayname_flat() : : Function : Makes all the sequences be displayed : as just their name, not name/start-end : : Returns : Argument : set_displayname_normal ---------------------- Title : set_displayname_normal Usage : $ali->set_displayname_normal() : : Function : Makes all the sequences be displayed : as name/start-end : : Returns : Argument : sort_alphabetically ------------------- Title : sort_alphabetically Usage : $ali->sort_alphabetically : : Function : changes the order of the alignemnt : to alphabetical on name followed by : numerical by number : Returns : Argument : uppercase --------- Title : uppercase() Usage : $ali->uppercase() : : Function : Sets all the sequences : to uppercase : : Returns : Argument : write_clustalw -------------- Title : write_clustalw Usage : $ali->write_clustalw : : Function : writes a clustalw formatted : (.aln) file : : Returns : Argument : write_fasta ----------- Title : write_fasta Usage : $ali->write_fasta(\*OUTPUT) : : Function : writes a fasta formatted alignment : Returns : Argument : reference-to-glob to file or filehandle object write_MSF --------- Title : write_MSF Usage : $ali->write_MSF(\*FH) : : Function : writes MSF format output : : : Returns : Argument : write_Pfam ---------- Title : write_Pfam Usage : $ali->write_Pfam(\*OUTPUT) : : Function : writes a Pfam/Mul formatted : file : : Returns : Argument : write_selex ----------- Title : write_selex Usage : $ali->write_selex(\*OUTPUT) : : Function : writes a selex (hmmer) formatted alignment : Returns : Argument : reference-to-glob to file or filehandle object  File: pm.info, Node: Bio/Species, Next: Bio/Tk/GO_Browser, Prev: Bio/SimpleAlign, Up: Module List Generic species object ********************** NAME ==== Bio::Species - Generic species object SYNOPSIS ======== $species = Bio::Species->new(-classification => [@classification]); # Can also pass classification # array to new as below $species->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota )); $genus = $species->genus(); $bi = $species->binomial(); # $bi is now "Homo sapiens" # For storing common name $species->common_name("human"); # For storing subspecies $species->sub_species("accountant"); DESCRIPTION =========== Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of nodes in a phylogenetic tree. Access to getting and setting species and genus is provided, but not to any of the other node types (eg: "phlum", "class", "order", "family"). There's plenty of scope for making the model more sophisticated, if this is ever needed. A methods are also provided for storing common names, and subspecies. CONTACT ======= 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 _ classification -------------- Title : classification Usage : $self->classification(@class_array); @classification = $self->classification(); Function: Fills or returns the classifcation list in the object. The array provided must be in the order SPECIES, GENUS ---> KINGDOM. Checks are made that species is in lower case, and all other elements are in title case. Example : $obj->classification(qw( sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota)); Returns : Classification array Args : Classification array common_name ----------- Title : common_name Usage : $self->common_name( $common_name ); $common_name = $self->common_name(); Function: Get or set the commonn name of the species Example : $self->common_name('human') Returns : The common name in a string Args : String, which is the common name species ------- Title : species Usage : $self->species( $species ); $species = $self->species(); Function: Get or set the scientific species name. The species name must be in lower case. Example : $self->species( 'sapiens' ); Returns : Scientific species name as string Args : Scientific species name as string genus ----- Title : genus Usage : $self->genus( $genus ); $genus = $self->genus(); Function: Get or set the scientific genus name. The genus must be in title case. Example : $self->genus( 'Homo' ); Returns : Scientific genus name as string Args : Scientific genus name as string sub_species ----------- Title : sub_species Usage : $obj->sub_species($newval) Function: Returns : value of sub_species Args : newvalue (optional) binomial -------- Title : binomial Usage : $binomial = $self->binomial(); $binomial = $self->binomial('FULL'); Function: Returns a string "Genus species", or "Genus species subspecies", the first argument is 'FULL' (and the species has a subspecies). Args : Optionally the string 'FULL' to get the full name including the the subspecies.  File: pm.info, Node: Bio/Tk/GO_Browser, Next: Bio/Tk/HitDisplay, Prev: Bio/Species, Up: Module List NAME ---- Bio::Tk::GO_Browser.pm - Simplistic browser for GO ontology terms AUTHORS ------- Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca) Plant Biotechnology Institute, National Research Council of Canada. Copyright (c) National Research Council of Canada, October, 2000. DISCLAIMER ---------- Anyone who intends to use and uses this software and code acknowledges and agrees to the following: The National Research Council of Canada (herein "NRC") disclaims any warranties, expressed, implied, or statutory, of any kind or nature with respect to the software, including without limitation any warranty or merchantability or fitness for a particular purpose. NRC shall not be liable in any event for any damages, whether direct or indirect, consequential or incidental, arising from the use of the software. SYNOPSIS -------- use GO_Browser; use Tk; use strict; Begin(); MainLoop; sub Begin { my $Textbox; my $GO; # create new main window. my $mw = MainWindow->new(-title => "GO Ontology Browser"); # create new textbox with scrollbars $Textbox = $mw->Scrolled("Text", -background => "black")->pack(-fill => "both", -expand => 1); # alternate method to create new textbox, NOT RECOMMENDED!! #$Textbox = $mw->Text(-background => "black")->pack; # create new GO browser $GO = GO_Browser->new($Textbox, TopWindow => $mw); # set up binding of button-2 to retrieve information $Textbox->bind("" => sub { my $acc = $GO->GOAcc; my $term = $GO->Term; my $def = $GO->Definition; print "Acc = $acc Term = $term Def = $def\n\n"; }); } DESCRIPTION and ACKNOWLEDGEMENTS -------------------------------- Fills a Tk::Text widget with a browsable display of the GO ontology (http://www.geneontology.org/). Items in red are "branches", while items in green are "leaves" of the GO ontology tree. Double-clicking branches moves you up and down the tree. Middle-clicking on any element records the clicked-upon term and definition (if available) and this event can be trapped by the top-level windowing system to retrieve this info for whatever external application you are building. Unlike previous versions, this browser connects directly to the GO ontology database. Therefore it requires no pre-downloading and parsing of the XML files (halleluja!) Because it is connecting "live" there is sometimes a small delay while the query is being sent over the net. The number of queries required for the browser has been mitigated as much as possible by some clever left-joins written by Dave Block (dblock@gene.pbi.nrc.ca). Thanks Dave! CONTACT ------- Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca) Options ------- $GO = GO_Browser->new( $Textbox, # the Tk Text widget TopWindow => $mw, # the top-level window (or undef) GO_IP => "headcase.lbl.gov", # the IP address of your GO database GO_dbName => "go" # the name of the GO database ); Methods ------- $GO->GOAcc # returns Accession number of the middle-clicked term $GO->Term # returns the Term name of the middle-clicked term $GO->Definition # returns the associated definition  File: pm.info, Node: Bio/Tk/HitDisplay, Next: Bio/Tk/SeqCanvas, Prev: Bio/Tk/GO_Browser, Up: Module List Frame-based widget for displaying Fasta or Blast hits/HSPs with optional text annotation **************************************************************************************** NAME ==== Bio::Tk::HitDisplay - Frame-based widget for displaying Fasta or Blast hits/HSPs with optional text annotation SYNOPSIS ======== use Bio::Tk::HitDisplay; ... $hds = $parent->HitDisplay(?options?); DESCRIPTION =========== *HitDisplay* is a Frame-based widget which contains a Canvas. When provided with a list of data structures, each representing a hit of a query sequence to a database, it draws: * A scale This is marked in residues (aa for a protein query, nt for a nucleic acid query) * The query sequence Represented as a single green line * Database hits A line for each Fasta hit, or a group of lines for each Blast hit (one per HSP) The coordinates of the hits/HSPs on the subject sequence (i.e. the sequence in the database) are indicated below the ends of each line. The *HitDisplay* delegates all standard options to the Canvas contained within it. The non-standard options for *HitDisplay* are: *-hitdata* => \@hitdata The structure of each element of this list is quite complex. They are normally generated from object(s) representing Blast or Fasta hits e.g. Bio::PSU::IO::Blast::Hit Bio::PSU::IO::Fasta::Hit by their respective adapters Bio::PSU::IO::Blast::HitAdapter Bio::PSU::IO::Fasta::HitAdapter This is normally hidden, unless you want to go and look. Each element is a reference to a hash containing the following keys and values: { q_id => 'query id', s_id => 'subject id', expect => 'expect value', score => 'percentage identity', overlap => 'length of hit', q_len => 'query length', s_len => 'subject length', data => \@data, text => "Some text", callback => $callback } @data is a list of references to lists, each of which contains the coordinates of a single Fasta hit or Blast HSP on both the query and subject sequences. Each innermost list contains 4 values; the start and end coordinates on the query sequence (indices 0 and 1) and the start and end coordinates on the subject sequence (indices 2 and 3). A Blast hit with 3 HSPs will look like this: [ [ q_start1, q_end1, s_start1, s_end1 ], [ q_start2, q_end2, s_start2, s_end2 ], [ q_start3, q_end3, s_start3, s_end3 ] ] The text field may contain any text which should be associated with that hit e.g. a more detailed account of the result or of the subject sequence. The display of this text is bound to a right mouse button click on the subject id in the canvas window. The text will appear just below the hit with one click and a subsequent click will hide it again. The callback is a code reference which, if defined, will be bound to a left mouse button click on the subject id in the canvas window. *-hitcolours* => \%colourhash The hits or HSPs will be colour-coded according to percentage identity according to the key->value pairs in the colourhash. The default values are: { 90 => 'red', 80 => 'orange', 60 => 'gold', 40 => 'yellow' } This indicates that hits where the query is >= 90% identical to the subject will be red, >= 80% will be orange etc. The hash supplied to *-hitcolours* will override the defaults. *-interval* => integer >= 10 This defines the vertical spacing between hit lines on the canvas. The minimum (and default) value is 10. Mouse bindings provided: * Vertical scrolling Wheel-mouse support is provided by binding buttons 4 and 5 to vertical scrolling (standard Z-axis mapping under XFree86 on Linux). * Panning Holding down the middle mouse button while dragging will pan the canvas in all directions * Display/hide all text annotations Double-clicking the left mouse button within the canvas will display all text annotations, while double-clicking with the right button will hide them. This is slow at the moment, with more than about 20 hits. Possible improvements: * Speed up opening/closing all text annotations at once * Items other than text between the hits * Make more of the canvas configurable Mouse bindings should be made configurable. Perhaps the canvas items making up each hit should be given a unique tag METHODS ======= Interaction with this widget should generally be by means of the standard Perl/Tk options. Internal methods are documented below. AUTHOR ====== Keith James (kdj@sanger.ac.uk) ACKNOWLEDGEMENTS ================ See Bio::PSU.pod COPYRIGHT ========= Copyright (C) 2000 Keith James. All Rights Reserved. DISCLAIMER ========== This module is provided "as is" without warranty of any kind. It may redistributed under the same conditions as Perl itself. Populate -------- Title : Populate Usage : N/A Function: Standard composite Frame-based widget setup. : See 'man Tk::composite' for details Returns : Nothing Args : Hash reference draw_align ---------- Title : draw_align Usage : N/A Function: Draws hit text, line and coords for the hits Returns : Nothing Args : Canvas, hitdata hash reference, left margin for text, : x coord for lines, y coord for lines, interval between : sets of lines (representing 1 Fasta hit or 1+ Blast : HSPs), hitcolours hash reference h_line ------ Title : h_line Usage : N/A Function: Draws a single hit/HSP line with the subject coords : below it Returns : Nothing Args : Canvas, hit hash reference, x coord for line, : y coord for line, line width, line colour draw_scale ---------- Title : draw_scale Usage : N/A Function: Draws scale alongside line representing query : sequence Returns : Nothing Args : Canvas, hit hash reference, left margin for text : x coord for line, y coord for line deannotate_hit -------------- Title : deannotate_hit Usage : N/A Function: Reverses the effect of annotate_hit Returns : Nothing Args : Canvas, text item (subject id), text to be inserted : in gap, interval between hits annotate_hit ------------ Title : annotate_hit Usage : N/A Function: Displays hit annotation below a hit line by shuffling : all canvas elements down the canvas and placing the : annotation text in the gap Returns : Nothing Args : Canvas, text item (subject id), text to be inserted : in gap, interval between hits  File: pm.info, Node: Bio/Tk/SeqCanvas, Next: Bio/Tools/AlignFactory, Prev: Bio/Tk/HitDisplay, Up: Module List AUTHORS ------- Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca), David Block (dblock@gene.pbi.nrc.ca) Plant Biotechnology Institute, National Research Council of Canada. Copyright (c) National Research Council of Canada, October, 2000. DISCLAIMER ---------- Anyone who intends to use and uses this software and code acknowledges and agrees to the following: The National Research Council of Canada (herein "NRC") disclaims any warranties, expressed, implied, or statutory, of any kind or nature with respect to the software, including without limitation any warranty or merchantability or fitness for a particular purpose. NRC shall not be liable in any event for any damages, whether direct or indirect, consequential or incidental, arising from the use of the software. SYNOPSIS -------- # To create a BioSeq map and return a handle to the map object: use Tk; Begin(); MainLoop; sub Begin { # set up the Tk Windows my $MW = MainWindow = MainWindow->new (-title => "Map Of BioSeq Object"); my $Frame = $MW->Frame()->pack(-side => 'top'); my $lblSysMess = $MW->Label()->pack(-side => 'bottom', -fill => 'both'); # create a BioSeq object my $SIO = Bio::SeqIO->new(-file=> 'genbankfile.gb', -format => 'GenBank'); my $SeqObj = $SIO->next_seq(); my $axis_length = 800; # how large I want the final map to be # Draw the Map $MapObj = SeqCanvas->new( $axis_length, $Frame, $lblSysMess, $SeqObj, -orientation => 'vertical' label => 'primary_id'); # SeqCanvas returns object reference for success # returns -1 for failed initiation - no $SeqObj supplied # returns -2 for bad sequence object # returns -3 sequence has length 0 # returns -4 if orientation is uninterpretable # returns -5 if supplied frame object is not a TK::frame } DESCRIPTION and ACKNOWLEDGEMENTS -------------------------------- Creates an interactive scalable/zoomable map of all features and subfeatures of a Bio::SeqI compliant object. Basic functionality for selecting single and multiple map objects is inherent in the object itself: left-mouse click to select, SHIFT-left-mouse to select multiple. All other Tk Events are passed back up to the MainWindow object and can be trapped/bound by the user as they see fit. Colors and axis-offsets of mapped objects are assigned based on the "source" tag of the feature object. These are assigned "on the fly" based on whatever is contained in the BioSeq object provided. This module requires an updated version of Gregg Helt's original BioTkPerl modules(version 0.81) which are available from BioPerl. The original BioTkPerl (version 0.80) is Copyright (c) Gregg Helt, 1995; Version 0.81 was generated by Mark Wilkinson, PBI-NRC, Oct., 2000. Zooming routines/events in this module are conceptually based on the Zoom routines from Genotator (Copyright (c) 1996, The Regents of the University of California. Harris, N.L. (1997), Genome Research 7(7):754-762) CONTACT ------- Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca) and Dave Block (dblock@gene.pbi.nrc.ca) APPENDIX -------- Description of Object tags, SeqCanvas Methods, and trapping Mouse events. Object Tags: ------------ Each map-widget has several "reliable" tags attached to it. These tags are FIDxxxx, Source and Strand, Type, and Canvas, where: * FIDxxxx is the unique identifier for that particular map-widget over all maps (even in multiple windows) * Source is derived from the "source" tag of the SeqFeature object this widget represents * Strand is derived from the "strand" tag of the SeqFeature object, converted into the GFF standard of +/-/. to represent the three possible strand values. * Type isthe feature type, derived from the primary_tag of the SeqFeature object * Map is either 'draft' or 'finished' to represent an object on the white or blue maps respectively So for example, a map widget might have the tags : FID22354 (no space) Source GeneMarkHMM (single space separated) Strand + (single space separated) Type exon ( " ) Canvas draft ( " ) If your BioSeq Features are being derived from an external database, it is possible to also include the unique index number of that database entry as a fourth tag on the associated map-widget. To do so, create your SeqFeature objects with an additional tag "id", where the unique databse index number is the value of this tag. This index number is then attached to the widget as a fourth tag with the form: DB_ID xxxxx (x's represent the unique index value) The values of these three/four tags can be retrieved for any selected object using the getSelectedTags function (see below) in order to relate mapped objects back to their original database entries. Using the selectWithTag or recolorWithTag routines (see below) requires that you pass the **full tag** as the desired selection (eg. pass "Source GeneMarkHMM" not just "GeneMarkHMM") METHODS ------- new --- Title : new Usage : $MapObj= SeqCanvas->new( $axis_length, $Frame, [$lblSysMess | undef], $SeqObj, -orientation => ['horizontal'|'vertical'] [, label => $tag]) Function : create a map from the Feature object provided Returns : Handle to the Map object Args : axis_length in pixels, a Tk::Frame object, a Tk::Label or undef, a BioSeqI compliant object, the orientation for the map, optionally the SeqFeature tag you wish to use as the label mapFeatures ----------- Title : mapFeatures Usage : $FeatureIDs = $MapObj->mapFeatures('draft'|'finished', \@FeatureObj) Function : map SeqFeature objects to the 'draft'(white) or 'finished' (blue) maps Returns : reference to a list of the FeatureID's of the mapped Features Args : 'draft'|'finished', \@FeatureObj unmapFeatures ------------- Title : unmapFeatures Usage : my $FeatureObjsRef = $MapObj->unmapFeatures(\@FeatureIDs) Function : to remove mapped features from the map display Returns : referenced list of removed $FeatureObj objects getSelectedIDs -------------- Title : getSelectedIDs Usage : $FeatureIDs = $MapObj->getSelectedIDs Function : to retrieve the FeatureID's of all currently selected mapped objects Returns : reference to a list of FeatureID's Args : none getSelectedTags --------------- Title : getSelectedTags Usage : ($FeatureID, $strand, $source, $type, $canvas [, $DB_ID]) = $MapObj->getSelectedTags Returns : FeatureID, Source, Strand, Type (i.e. Primary_tag), Canvas ('draft' or 'finished'), and Database_Index (if available). Comment : This is to be used for single-selection events only! Args : none getIDsWithTag Title : getIDsWithTag Usage : $FeatureIDs = $MapObj->getIDsWithTag(\@taglist) Function : to retrieve the FeatureID's of all currently selected mapped objects Returns : reference to a list of FeatureID's Args : a reference to a list of tags (see discussion of proper tag format above) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ getSelectedFeatures ------------------- Title : getSelectedFeatures Usage : $FeatureHashRef = $MapObj->getSelectedFeatures Returns : a reference to a hash where the FeatureID is the key, and the Bio::SeqFeature Object is the value Args : none getFeaturesWithTag ------------------ Title : getFeaturesWithTag Usage : $FeatureHashRef = $MapObj->getFeaturesWithTag(\@taglist) Returns : a reference to a hash where the FeatureID is the key, and the Bio::SeqFeature Object is the value Args : reference to a list of valid tags (see discussion of proper tag format) clearSelections --------------- Title : clearSelections Usage : $MapObj->clearSelections Function : Clear all selection boxes and "selected" status of all Features. Returns : nothing Args : none selectFeatures -------------- Title : selectFeatures Usage : $MapObj->selectFeatures(\@FeatureIDs) Function : "select" all Features with @FeatureID id's Args : @FeatureIDs - a list of valid FeatureIDs (of the form FIDnnn where nnn is a unique integer) selectWithTag ------------- Title : selectWithTag Usage : $MapObj->selectWithTag(\@tag_list [,'draft'|'finished']) Function : "select" all features which have any of @tag_list tags. Args : @taglist, and optional 'draft' or 'finished' which map recolorWithTag -------------- Title : recolorWithTag Usage : $MapObj->recolorWithTag('#XXXXXX'|'default', 'draft'|'finished', \@tag_list) Function : change the color of mapped objects having one of @tag_list tags. Returns : nothing Args : First arg:hex-reference to an RGB color value, or 'default'. Second arg: the canvas ('draft', or 'finished') Third arg: a referenced list of tags. assignCustomColors ------------------ Title : assignCustomColors Usage : $MapObj->assignCustomColors($top) Function : change the default map-color for a selected widgets "Source" tag. Returns : nothing Args : a reference to a Tk::MainWindow object (new or existing). is_draft_feature ---------------- Title : is_draft_feature Usage : $result = $MapObj->is_draft_feature($FeatureID) Function : check if a $FeatureID is on the draft (white) map. Returns : 1 for true, undef for false Args : the FeatureID you are querying is_finished_feature ------------------- Title : is_finished_feature Usage : $result = $MapObj->is_finished_feature($FeatureID) Function : check if $FeatureID is on the finished (blue) map. Returns : 1 for true, undef for false Args : the FeatureID you are querying EVENTS ====== The SeqCanvas both internally responds to mouse events, and sets "tags" on the mapped feature in response to mouse events such that the user can "trap" these events in the top-level windowing system and evaluate which mapped feature the user was manupulating. Mouse-Click ----------- Clicking or shift-Clicking the left mouse button over a mapped feature causes the feature(s) to become "selected". A selected object is displayed on the screen with a black box surrounding the object, and the object becomes tagged with a testable tag "selected" (use the getSelectedFeatures or getSelectedIDs to retrieve additional information about this object) Mouse-Double-Click ------------------ Both Double-clicking and Shift Double-Clicking the mouse over an object selects that (single) mapped feature. All other features become unselected. Mouse-Click and Drag -------------------- Used to select multiple objects. Any object touched by the bounding box will be included in the selection. Mouse-Over ---------- As the mouse pointer enters the mapped widget, the tag "Mouse_over" is added to this object. information about this object could be retrieved by, for example, calling the getIDsWithTag(["Mouse_over"]) method. This tag is removed when the mouse pointer leaves the mapped-feature space. Bind the event in the top-level windowing system to track the mouse movements if you wish to monitor the Mouse-Over widget events.