This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/SeqI, Next: Bio/SeqIO, Prev: Bio/SeqFeatureI, Up: Module List Abstract Interface of Sequence (with features) ********************************************** NAME ==== Bio::SeqI - Abstract Interface of Sequence (with features) SYNOPSIS ======== # get a Bio::SeqI somehow, eg, via SeqIO. See SeqIO info # for more information $seqio = Bio::SeqIO->new ( '-format' => 'Fasta' , -file => 'myfile.fasta'); $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 =========== SeqI is the abstract interface of annotated Sequence. These methods are those which you can be guarenteed to get for any annseq. There aren't many here, because too many complicated functions here prevent implementations which are just wrappers around a database or similar delayed mechanisms. Most of the clever stuff happens inside the SeqFeatureI system. A good reference implementation is Bio::Seq which is a pure perl implementation of this class with alot of extra pieces for extra manipulation. However, if you want to be able to use any sequence object in your analysis, if you can do it just using these methods, then you know you will be future proof and compatible with other implementations of Seq. 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@sanger.ac.uk APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ top_SeqFeatures --------------- Title : top_SeqFeatures Usage : Function: Example : Returns : Args : all_SeqFeatures --------------- Title : all_SeqFeatures Usage : @features = $annseq->all_SeqFeatures() Function: returns all SeqFeatures, included sub SeqFeatures Returns : an array Args : none seq --- Title : seq Usage : Function: Example : Returns : Args : write_GFF --------- Title : write_GFF Usage : Function: Example : Returns : Args : annotation ---------- Title : annotation Usage : $obj->annotation($seq_obj) Function: Example : Returns : value of annotation Args : newvalue (optional) primary_seq ----------- Title : primary_seq Usage : $obj->primary_seq($newval) Function: Example : Returns : value of primary_seq Args : newvalue (optional) 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/SeqIO, Next: Bio/SeqIO/EMBL, Prev: Bio/SeqI, Up: Module List Handler for SeqIO Formats ************************* NAME ==== Bio::SeqIO - Handler for SeqIO Formats SYNOPSIS ======== use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "inputfilename" , '-format' => 'Fasta'); $out = Bio::SeqIO->new(-file => ">outputfilename" , '-format' => 'EMBL'); # note: we quote -format to keep older perl's from complaining. while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); } or use Bio::SeqIO; $in = Bio::SeqIO->newFh(-file => "inputfilename" , '-format' => 'Fasta'); $out = Bio::SeqIO->newFh('-format' => 'EMBL'); # World's shortest Fasta<->EMBL format converter: print $output $_ while <$in>; DESCRIPTION =========== Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The SeqIO system replaces the old parse_XXX functions in the Seq object. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular SeqIO object instance is configured for either input or output. A specific example of a stream object is the Bio::SeqIO::fasta object. Each stream object has functions $stream->next_seq(); and $stream->write_seq($seq); also $stream->type() # returns 'INPUT' or 'OUTPUT' As an added bonus, you can recover a filehandle that is tied to the SeqIO object, allowing you to use the standard <> and print operations to read and write sequence objects: use Bio::SeqIO; $stream = Bio::SeqIO->newFh(-format => 'Fasta'); # read from standard input while ( $seq = <$stream> ) { # do something with $seq } and print $stream $seq; # when stream is in output mode This makes the simplest ever reformatter #!/usr/local/bin/perl $format1 = shift; $format2 = shift || die "Usage: reformat format1 format2 < input > output"; use Bio::SeqIO; $in = Bio::SeqIO->newFh(-format => $format1 ); $out = Bio::SeqIO->newFh(-format => $format2 ); #note: you might want to quote -format to keep older perl's from complaining. print $out $_ while <$in>; CONSTRUCTORS ============ Bio::SeqIO->new() ----------------- $seqIO = Bio::SeqIO->new(-file => 'filename', -format=>$format); $seqIO = Bio::SeqIO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::SeqIO->new(-format => $format); The new() class method constructs a new Bio::SeqIO object. The returned object can be used to retrieve or print BioSeq objects. new() accepts the following parameters: -file A file path to be opened for reading or writing. The usual Perl conventions apply: 'file' # open file for reading '>file' # open file for writing '>>file' # open file for appending '+new(-fh => \*STDIN); Note that you must pass filehandles as references to globs. If neither a filehandle nor a filename is specified, then the module will read from the @ARGV array or STDIN, using the familiar <> semantics. -format Specify the format of the file. Supported formats include: Fasta FASTA format EMBL EMBL format GenBank GenBank format swiss Swissprot format SCF SCF tracefile format PIR Protein Information Resource format GCG GCG format raw Raw format (one sequence per line, no ID) ace ACeDB sequence format If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, Fasta format is assumed. The format name is case insensitive. 'FASTA', 'Fasta' and 'fasta' are all supported. Bio::SeqIO->newFh() ------------------- $fh = Bio::SeqIO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::SeqIO->newFh(-format => $format); # etc. This constructor behaves like new(), but returns a tied filehandle rather than a Bio::SeqIO object. You can read sequences from this object using the familiar <> operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this: @sequences = <$fh>; Other operations, such as read(), sysread(), write(), close(), and printf() are not supported. OBJECT METHODS ============== See below for more detailed summaries. The main methods are: $sequence = $seqIO->next_seq() ------------------------------ Fetch the next sequence from the stream. $seqIO->write_seq($sequence [,$another_sequence,...]) ----------------------------------------------------- Write the specified sequence(s) to the stream. TIEHANDLE(), READLINE(), PRINT() -------------------------------- These provide the tie interface. See *Note Perltie: (perl.info)perltie, for more details. 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@bioperl.org http://bioperl.org/bioperl-bugs/ AUTHOR - Ewan Birney, Lincoln Stein =================================== 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 : $stream = Bio::SeqIO->new(-file => $filename, -format => 'Format') Function: Returns a new seqstream Returns : A Bio::SeqIO::Handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to newFh ----- Title : newFh Usage : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format') $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::SeqIO::Fh class Args : fh -- Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::SeqIO::Fh class Args : next_seq -------- Title : next_seq Usage : $seq = stream->next_seq Function: Reads the next sequence object from the stream and returns it. Certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable, e.g., by dismissing a feature of a feature table or some other non-mandatory part of an entry, the driver will issue a warning. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2) (see Bio::RootI POD page). Returns : a Bio::Seq sequence object Args : next_primary_seq ---------------- Title : next_primary_seq Usage : $seq = $stream->next_primary_seq Function: Provides a primaryseq type of sequence object Returns : A Bio::PrimarySeqI 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 moltype ------- Title : moltype Usage : $self->moltype($newval) Function: Set/get the molecule type for the Seq objects to be created. Example : $seqio->moltype('protein') Returns : value of moltype: 'dna', 'rna', or 'protein' Args : newvalue (optional) Throws : Exception if the argument is not one of 'dna', 'rna', or 'protein' _load_format_module ------------------- Title : _load_format_module Usage : *INTERNAL SeqIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : _concatenate_lines ------------------ Title : _concatenate_lines Usage : $s = _concatenate_lines($line, $continuation_line) Function: Private. Concatenates two strings assuming that the second stems from a continuation line of the first. Adds a space between both unless the first ends with a dash. Takes care of either arg being empty. Example : Returns : A string. Args : _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: This method is deprecated. Call _fh() instead. Example : Returns : value of _filehandle Args : newvalue (optional) _guess_format ------------- Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :  File: pm.info, Node: Bio/SeqIO/EMBL, Next: Bio/SeqIO/FTHelper, Prev: Bio/SeqIO, Up: Module List EMBL sequence input/output stream ********************************* NAME ==== Bio::SeqIO::EMBL - EMBL 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 => 'EMBL'); while $seq ( <$stream> ) { # $seq is a Bio::Seq object } DESCRIPTION =========== This object can transform Bio::Seq objects to and from EMBL 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. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney ==================== Email birney@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 _ 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 _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)  File: pm.info, Node: Bio/SeqIO/FTHelper, Next: Bio/SeqIO/Fasta, Prev: Bio/SeqIO/EMBL, Up: Module List Helper class for Embl/Genbank feature tables ******************************************** NAME ==== Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables SYNOPSIS ======== Used by Bio::SeqIO::EMBL to help process the Feature Table DESCRIPTION =========== Represents one particular Feature with the following fields key - the key of the feature loc - the location string of the feature - other fields 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/ 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 _ _generic_seqfeature ------------------- Title : _generic_seqfeature Usage : $fthelper->_generic_seqfeature($annseq, "GenBank") Function: processes fthelper into a generic seqfeature Returns : TRUE on success and otherwise FALSE Args : Bio::Seq, string indicating the source (GenBank/EMBL/SwissProt) _parse_loc ---------- Title : _parse_loc Usage : $fthelper->_parse_loc( $loc_string) Function: Parses the given location string and returns a location object with start() and end() and strand() set appropriately. Note that this method is private. Returns : location object or 0 on fail Args : location string from_SeqFeature --------------- Title : from_SeqFeature Usage : @fthelperlist = Bio::SeqIO::FTHelper::from_SeqFeature($sf, $context_annseq); Function: constructor of fthelpers from SeqFeatures : : The additional annseq argument is to allow the building of FTHelper : lines relevant to particular sequences (ie, when features are spread over : enteries, knowing how to build this) Returns : an array of FThelpers Args : seq features key --- Title : key Usage : $obj->key($newval) Function: Example : Returns : value of key Args : newvalue (optional) loc --- Title : loc Usage : $obj->loc($newval) Function: Example : Returns : value of loc Args : newvalue (optional) field ----- Title : field Usage : Function: Example : Returns : Args : add_field --------- Title : add_field Usage : Function: Example : Returns : Args :  File: pm.info, Node: Bio/SeqIO/Fasta, Next: Bio/SeqIO/GCG, Prev: Bio/SeqIO/FTHelper, Up: Module List Fasta sequence input/output stream ********************************** NAME ==== Bio::SeqIO::Fasta - Fasta 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 => 'Fasta'); while $seq ( <$stream> ) { # $seq is a Bio::Seq object } 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. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney ==================== Email birney@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 _ 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 _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)  File: pm.info, Node: Bio/SeqIO/GCG, Next: Bio/SeqIO/Handler, Prev: Bio/SeqIO/Fasta, Up: Module List Raw sequence input/output stream ******************************** NAME ==== Bio::SeqIO::GCG - Raw 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 => 'GCG'); while $seq ( <$stream> ) { # $seq is a Bio::Seq object } DESCRIPTION =========== This object can transform Bio::Seq objects to and from GCG-formatted sequence 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. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHORS - Ewan Birney & Chris Dagdigian ======================================= Email birney@sanger.ac.uk, dag@sonsorol.org Ewan Birney wrote the all the base SeqIO stuff. This module is based on his SeqIO::Fasta and has been tweaked by Chris Dagdigian, to support GCG formatted sequence input/output. 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 fromatted $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object, sequence string _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) _validate_checksum ------------------ Title : _validate_checksum Usage : n/a - internal method Function: if parsed gcg sequence contains a checksum field : we compare it to a value computed here on the parsed : sequence. A checksum mismatch would indicate some : type of parsing failure occured. : Returns : 1 for success, 0 for failure Args : string containing parsed seq, value of parsed cheksum  File: pm.info, Node: Bio/SeqIO/Handler, Next: Bio/SeqIO/MultiFile, Prev: Bio/SeqIO/GCG, Up: Module List Handler of the SeqIO classes for tieing to filehandles ****************************************************** NAME ==== Bio::SeqIO::Handler - Handler of the SeqIO classes for tieing to filehandles SYNOPSIS ======== $stream = Bio::SeqIO->new(-file => "filename", -format => 'Fasta'); tie *SEQ, 'Bio::SeqIO::Handler', $stream; while $seq ( ) { # $seq is Bio::Seq object } DESCRIPTION =========== This object wraps over the Bio::SeqIO:: format classes, providing the correct glue for the tie mechanism in to filehandles. This allows normal looking perl filehandles can be used to provide a streams for converting sequences to and from ascii formats FEEDBACK ======== Mailing Lists ------------- User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney ==================== Email birney@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 _ _streamobj ---------- Title : _streamobj Usage : $obj->_streamobj($newval) Function: Example : Returns : value of _streamobj Args : newvalue (optional)  File: pm.info, Node: Bio/SeqIO/MultiFile, Next: Bio/SeqIO/Raw, Prev: Bio/SeqIO/Handler, Up: Module List Treating a set of files as a single input stream ************************************************ NAME ==== Bio::SeqIO::MultiFile - Treating a set of files as a single input stream SYNOPSIS ======== $seqin = Bio::SeqIO::MultiFile( '-format' => 'Fasta', '-files' => ['file1','file2'] ); while((my $seq = $seqin->next_seq)) { # do something with $seq } DESCRIPTION =========== Bio::SeqIO::MultiFile provides a simple way of bundling a whole set of identically formatted sequence input files as a single stream. 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/ 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 _ next_seq -------- Title : next_seq Usage : Function: Example : Returns : Args : next_primary_seq ---------------- Title : next_primary_seq Usage : Function: Example : Returns : Args : _load_file ---------- Title : _load_file Usage : Function: Example : Returns : Args : _set_file --------- Title : _set_file Usage : Function: Example : Returns : Args : _current_seqio -------------- Title : _current_seqio Usage : $obj->_current_seqio($newval) Function: Example : Returns : value of _current_seqio Args : newvalue (optional) _format ------- Title : _format Usage : $obj->_format($newval) Function: Example : Returns : value of _format Args : newvalue (optional)  File: pm.info, Node: Bio/SeqIO/Raw, Next: Bio/SeqIO/ace, Prev: Bio/SeqIO/MultiFile, Up: Module List Raw sequence input/output stream ******************************** NAME ==== Bio::SeqIO::Raw - Raw 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 => 'Raw'); while $seq ( <$stream> ) { # $seq is a Bio::Seq object } DESCRIPTION =========== This object can transform Bio::Seq objects to and from raw textfiles. "Raw" is defined to mean 1 or more sequences separated by a newline. Raw sequences are just lines of data with no formatting or special fields. The write_seq() method has not been tested yet, should be simple enough. FEEDBACK ======== Mailing Lists ------------- User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists Reporting Bugs -------------- Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Ewan Birney ==================== Email birney@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 _ 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 _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)  File: pm.info, Node: Bio/SeqIO/ace, Next: Bio/SeqIO/embl, Prev: Bio/SeqIO/Raw, Up: Module List ace sequence input/output stream ******************************** NAME ==== Bio::SeqIO::ace - ace 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 ace file format. It only parses a DNA or Peptide objects contained in the ace file, producing PrimarySeq objects from them. All other objects in the files will be ignored. It doesn't attempt to parse any annotation attatched to the containing Sequence or Protein objects, which would probably be impossible, since everyone's ACeDB schema can be different. It won't parse ace files containing Timestamps correctly either. This can easily be added if considered necessary. 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 - 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 _ next_primary_seq ---------------- Title : next_primary_seq Usage : $seq = $stream->next_primary_seq() Function: returns the next sequence in the stream Returns : Bio::PrimarySeq object Args : NONE next_seq -------- Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq 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(s)  File: pm.info, Node: Bio/SeqIO/embl, Next: Bio/SeqIO/fasta, Prev: Bio/SeqIO/ace, Up: Module List EMBL sequence input/output stream ********************************* NAME ==== Bio::SeqIO::embl - EMBL sequence input/output stream SYNOPSIS ======== It is probably best not to use this object directly, but rather go through the AnnSeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL'); while ( (my $seq = $stream->next_seq()) ) { # do something with $seq } DESCRIPTION =========== This object can transform Bio::Seq objects to and from EMBL flat file databases. There is alot of flexibility here about how to dump things which I need to document fully. There should be a common object that this and genbank share (probably with swissprot). Too much of the magic is identical. 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 ", $func($annseq), "\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://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/ 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 _ 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 _print_EMBL_FTHelper -------------------- Title : _print_EMBL_FTHelper Usage : Function: Example : Returns : Args : _read_EMBL_Species ------------------ Title : _read_EMBL_Species Usage : Function: Reads the EMBL Organism species and classification lines. Example : Returns : A Bio::Species object Args : _read_EMBL_DBLink ----------------- Title : _read_EMBL_DBLink Usage : Function: Reads the EMBL database cross reference ("DR") lines Example : Returns : A list of Bio::Annotation::DBLink objects Args : _filehandle ----------- Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional) _read_FTHelper_EMBL ------------------- Title : _read_FTHelper_EMBL Usage : _read_FTHelper_EMBL($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar _write_line_EMBL ---------------- Title : _write_line_EMBL Usage : Function: internal function Example : Returns : Args : _write_line_EMBL_regex ---------------------- Title : _write_line_EMBL_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/SeqIO/fasta, Next: Bio/SeqIO/game, Prev: Bio/SeqIO/embl, Up: Module List fasta sequence input/output stream ********************************** NAME ==== Bio::SeqIO::fasta - fasta 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://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 ===================================== Email: birney@ebi.ac.uk 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 : 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/game, Next: Bio/SeqIO/gcg, Prev: Bio/SeqIO/fasta, Up: Module List Parses GAME XML 0.1 and higher into and out of Bio::Seq objects. **************************************************************** NAME ==== Bio::SeqIO::game - Parses GAME XML 0.1 and higher into and out of Bio::Seq objects. SYNOPSIS ======== To use this module you need XML::Parser, XML::Parser::PerlSAX and XML::Writer. Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION =========== This object can transform Bio::Seq objects to and from bioxml seq, computation, feature and annotation dtds,versions 0.1 and higher. These can be found at http://www.bioxml.org/dtds/current. It does this using the idHandler, seqHandler and featureHandler modules you should have gotten with this one. The idea is that any bioxml features can be turned into bioperl annotations. When Annotations and computations are parsed in, they gain additional info in the bioperl SeqFeature tag attribute. These can be used to reconstitute a computation or annotation by the bioxml with the bx-handler module when write_seq is called. If you use this to write SeqFeatures that were not generated from computations or annotations, it will output a list of bioxml features. Some data may be lost in this step, since bioxml features just have a span, type and description - nothing about the anlysis performed. 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. bioxml-dev@bioxml.org - Technical discussion - Moderate volume bioxml-announce@bioxml.org - General Announcements - Pretty dead http://www.bioxml.org/MailingLists/ - About the mailing lists AUTHOR - Brad Marshall & Ewan Birney & Lincoln Stein ==================================================== Email: bradmars@yahoo.com birney@sanger.ac.uk lstein@cshl.org APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ _export_subfeatures ------------------- Title : _export_subfeatures Usage : $obj->_export_subfeatures Function: export all subfeatures (also in the geneprediction structure) Returns : value of _export_subfeatures Args : newvalue (optional) _group_subfeatures ------------------ Title : _group_subfeatures Usage : $obj->_group_subfeatures Function: Groups all subfeatures in separate feature_sets Returns : value of _group_subfeatures Args : newvalue (optional) _subfeature_types ----------------- Title : _subfeature_types Usage : $obj->_subfeature_types Function: array of all possible subfeatures, it should be a name of a function which : returns an arrau of sub_seqfeatures when called: @array = $feature->subfeaturetyp() Returns : array of _subfeature_types Args : array of subfeature types (optional) _add_subfeature_type Title : _add_subfeature_type Usage : $obj->_add_subfeature_type Function: add one possible subfeature, it should be a name of a function which : returns an arrau of sub_seqfeatures when called: @array = $feature->subfeaturetyp() Returns : 1 Args : one subfeature type (optional) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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_primary_seq Usage : $seq = $stream->next_primary_seq() Function: returns the next primary sequence (ie no seq_features) in the stream Returns : Bio::PrimarySeq object Args : NONE write_seq --------- Title : write_seq Usage : Not Yet Implemented! $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/gcg, Next: Bio/SeqIO/genbank, Prev: Bio/SeqIO/game, Up: Module List GCG sequence input/output stream ******************************** NAME ==== Bio::SeqIO::gcg - GCG 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 GCG 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 ===================================== Email: birney@ebi.ac.uk 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 fromatted $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object, sequence string GCG_checksum ------------ Title : GCG_checksum Usage : $cksum = $gcgio->GCG_checksum($seq); Function : returns a gcg checksum for the sequence specified This method can also be called as a class method. Example : Returns : a GCG checksum string Argument : a Bio::PrimarySeqI implementing object _validate_checksum ------------------ Title : _validate_checksum Usage : n/a - internal method Function: if parsed gcg sequence contains a checksum field : we compare it to a value computed here on the parsed : sequence. A checksum mismatch would indicate some : type of parsing failure occured. : Returns : 1 for success, 0 for failure Args : string containing parsed seq, value of parsed cheksum  File: pm.info, Node: Bio/SeqIO/genbank, Next: Bio/SeqIO/largefasta, Prev: Bio/SeqIO/gcg, Up: Module List GenBank sequence input/output stream ************************************ NAME ==== Bio::SeqIO::GenBank - GenBank 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 => 'GenBank'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } DESCRIPTION =========== This object can transform Bio::Seq objects to and from GenBank 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. 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/ 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 $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : Bio::Seq _print_GenBank_FTHelper ----------------------- Title : _print_GenBank_FTHelper Usage : Function: Example : Returns : Args : _read_GenBank_References ------------------------ Title : _read_GenBank_References Usage : Function: Reads references from GenBank format. Internal function really Example : Returns : Args : _read_GenBank_Species --------------------- Title : _read_GenBank_Species Usage : Function: Reads the GenBank Organism species and classification lines. Example : Returns : A Bio::Species object Args : _read_FTHelper_GenBank ---------------------- Title : _read_FTHelper_GenBank Usage : _read_FTHelper_GenBank($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar _write_line_GenBank ------------------- Title : _write_line_GenBank Usage : Function: internal function Example : Returns : Args : _write_line_GenBank_regex ------------------------- Title : _write_line_GenBank_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)