| Bio::LiveSeq::Mutation(3pm) | User Contributed Perl Documentation | Bio::LiveSeq::Mutation(3pm) |
Bio::LiveSeq::Mutation - Mutation event descriptor class
# full description of a point mutation
$mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A',
-seqori => 'T',
-pos => 100,
-len => 1 # optional, defaults to length(seq)
);
# minimal information for a point mutation
$mutation1b = Bio::LiveSeq::Mutation->new ( -seq => 'A',
-pos => 100
);
# insertion
$mutation2 = Bio::LiveSeq::Mutation->new ( -seq => 'ATT',
-pos => 100,
-len => 0
);
# deletion
$mutation3 = Bio::LiveSeq::Mutation->new ( -seq => '', # optional
-seqori => 'TTG', # optional
-pos => 100
-len => 3
);
# complex
$mutation4 = Bio::LiveSeq::Mutation->new ( -seq => 'CC',
-seqori => 'TTG', # optional
-pos => 100
-len => 3
);
This class describes a local mutation event using minimalistic description. It is not necessary to know anything about the original sequence. You need to give the changed sequence, the position of the mutation in the (unidentified) reference sequence, and the length of the affected subsequence in the reference sequence. If the original allele sequence is given, the objects applying the mutation into the reference sequence (e.g. Bio::LiveSeq::Mutator) might check for its validity.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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
Email: heikki-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : seq
Usage : $obj->seq();
Function:
Sets and returns the mutated sequence. No checking is done
to validate the symbols.
Example :
Returns : string
Args : integer
Title : seqori
Usage : $obj->seqori();
Function:
Sets and returns the original subsequence in the reference
sequence. No checking is done to validate the symbols.
Optional value.
Example :
Returns : string
Args : string
Title : pos
Usage : $obj->pos();
Function:
Sets and returns the position of the first element in the
sequence.
Example :
Returns : string
Args : integer
Title : len
Usage : $obj->len();
Function:
Sets and returns the len of the affected original allele
sequence. If value is not set, defaults to the length of
the mutated sequence (seq).
Example :
Returns : string
Args : string
Title : label
Usage : $obj->label();
Function:
Sets and returns the label of the affected original allele
location. Label is a stable identifier whereas location
can be changed by mutations. Label comes from
l<Bio::LiveSeq::Gene>.
Example :
Returns : string
Args : string
Title : transpos
Usage : $obj->transpos();
Function:
Sets and returns the transcript position of the mutation.
Set when associated with a reference sequence. Value
depends on reference molecule and the co-ordinate system
used.
Example :
Returns : string
Args : integer
Title : issue
Usage : $obj->issue();
Function:
Sets and returns the position of the mutation in an array
of mutations to be issued. Set after the validity of the
mutation has been confirmed.
Example :
Returns : string
Args : integer
Title : prelabel
Usage : $obj->prelabel();
Function:
Sets and returns the prelabel of the affected original allele
location. Prelabel is a stable identifier whereas location
can be changed by mutations. Prelabel comes from
l<Bio::LiveSeq::Gene>.
Example :
Returns : string
Args : string
Title : postlabel
Usage : $obj->postlabel();
Function:
Sets and returns the postlabel of the affected original allele
location. Postlabel is a stable identifier whereas location
can be changed by mutations. Postlabel comes from
l<Bio::LiveSeq::Gene>.
Example :
Returns : string
Args : string
Title : lastlabel
Usage : $obj->lastlabel();
Function:
Sets and returns the lastlabel of the affected original allele
location. Lastlabel is a stable identifier whereas location
can be changed by mutations. Lastlabel comes from
l<Bio::LiveSeq::Gene>.
Example :
Returns : string
Args : string
| 2018-10-27 | perl v5.26.2 |