Bio::Restriction::IO::base(3pm) | User Contributed Perl Documentation | Bio::Restriction::IO::base(3pm) |
Bio::Restriction::IO::base - base enzyme set
Do not use this module directly. Use it via the Bio::Restriction::IO class.
This class defines some base methods for restriction enzyme input and at the same time gives a base list of common enzymes.
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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Rob Edwards, redwards@utmem.edu
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : read Usage : $renzs = $stream->read Function: reads all the restrction enzymes from the stream Returns : a Bio::Restriction::Restriction object Args : none
Title : _xln_sub Function: Translates withrefm coords to Bio::Restriction coords Args : Bio::Restriction::Enzyme object, scalar integer (cut posn) Note : Used internally; pass as a coderef to the B:R::Enzyme constructor Note : It is convenient for each format module to have its own version of this; not currently demanded by the interface.
Title : write Usage : $stream->write($renzs) Function: writes restriction enzymes into the stream Returns : 1 for success and 0 for error Args : a Bio::Restriction::Enzyme or a Bio::Restriction::EnzymeCollection object
Title : verify_prototype Purpose : checks enzyme against current prototype list (retrieved remotely) Returns : returns TRUE if enzyme is prototype Argument : Bio::Restriction::EnzymeI Comments : This is an auxiliary method to retrieve and check an enzyme as a prototype. It retrieves the current list, stores it as a singleton instance, then uses it to check the prototype and modify is_prototype() to true or false. Use as follows: my $col = $io->read; for my $enz ($col->each_enzyme) { print $enz->name.":".$enz->site."\n"; print "\t".$io->verify_prototype($enz)."\n"; }
The rest of the methods in this file are to be used by other REBASE parsers. They are not to be used outside subclasses of this base class. (They are 'protected' in the sense the word is used in Java.)
Title : _cuts_from_site Usage : ($site, $cut, $comp_cut) = _cuts_from_site('ACGCGT(4/5)'); Function: Separates cut positions from a single site string. Does nothing to site if it does not have the cut string Returns : array of site_string, forward_cut_position, reverse_cut_position Args : recognition site string Note : Not used in withrefm refactor/maj
Title : _meth Usage : ($pos, $meth) = $self->_meth('2(5)'); Function: Separates methylation position and coce from a string. Adjusts the position depending on enzyme site length and symmetry Returns : array of position and methylation code Args : 1. reference to Enzyme object 2. methylation description string
Title : _coordinate_shift_to_cut Usage : $cut = $self->_coordinate_shift_to_cut($oricut, offset); Function: Adjust cut position coordinates to start from the first nucleotides of site Returns : Cut position in correct coordinates Args : 1. Original cut position 2. Length of the recognition site Note : Not used in withrefm.pm refactor/maj
Title : _make_multisites Usage : $self->_make_multisites($first_enzyme, \@sites, \@mets) Function: Bless a Bio::Restriction::Enzyme into Bio::Restriction::Enzyme::MultiSite and clone it as many times as there are alternative sites. Returns : nothing, does in place editing Args : 1. a Bio::Restriction::Enzyme 2. reference to an array of recognition site strings 3. reference to an array of methylation code strings, optional
Title : _make_multicuts Usage : $self->_make_multicuts($first_enzyme, $precuts) Function: Bless a Bio::Restriction::Enzyme into Bio::Restriction::Enzyme::MultiCut and clone it. The precut string is processed to replase the cut sites in the cloned object. Both objects refer to each other through others() method. Returns : nothing, does in place editing Args : 1. a Bio::Restriction::Enzyme 2. precut string, e.g. '12/7'
The examples we have of multiply cutting enzymes cut only four times. This protected method deals only with a string of two integers separated with a slash, e.g. '12/7'. The numbers represent the positions BEFORE the start of the recognition site, i.e. negative positions.
Title : _companies Purpose : Defines the companies that we know about Returns : A hash Argument : Nothing Comments : An internal method to define the companies that we know about REBASE uses a code, and this converts the code to the real name (e.g. A = Amersham Pharmacia Biotech)
2018-10-27 | perl v5.26.2 |