NAME¶
Bio::LiveSeq::Mutator - Package mutating LiveSequences
SYNOPSIS¶
# $gene is a Bio::LiveSeq::Gene object
my $mutate = Bio::LiveSeq::Mutator->new('-gene' => $gene,
'-numbering' => "coding"
);
# $mut is a Bio::LiveSeq::Mutation object
$mutate->add_Mutation($mut);
# $results is a Bio::Variation::SeqDiff object
my $results=$mutate->change_gene();
if ($results) {
my $out = Bio::Variation::IO->new( '-format' => 'flat');
$out->write($results);
}
DESCRIPTION¶
This class mutates Bio::LiveSeq::Gene objects and returns a
Bio::Variation::SeqDiff object. Mutations are described as
Bio::LiveSeq::Mutation objects. See Bio::LiveSeq::Gene,
Bio::Variation::SeqDiff, and Bio::LiveSeq::Mutation for details.
FEEDBACK¶
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
Support¶
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.
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 the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Heikki Lehvaslaiho & Joseph A.L. Insana¶
Email: heikki-at-bioperl-dot-org
insana@ebi.ac.uk, jinsana@gmx.net
APPENDIX¶
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
gene¶
Title : gene
Usage : $mutobj = $obj->gene;
: $mutobj = $obj->gene($objref);
Function:
Returns or sets the link-reference to a
Bio::LiveSeq::Gene object. If no value has ben set, it
will return undef
Returns : an object reference or undef
Args : a Bio::LiveSeq::Gene
See Bio::LiveSeq::Gene for more information.
numbering¶
Title : numbering
Usage : $obj->numbering();
Function:
Sets and returns coordinate system used in positioning the
mutations. See L<change_gene> for details.
Example :
Returns : string
Args : string (coding [transcript number] | gene | entry)
add_Mutation¶
Title : add_Mutation
Usage : $self->add_Mutation($ref)
Function: adds a Bio::LiveSeq::Mutation object
Example :
Returns :
Args : a Bio::LiveSeq::Mutation
See Bio::LiveSeq::Mutation for more information.
each_Mutation¶
Title : each_Mutation
Usage : foreach $ref ( $a->each_Mutation )
Function: gets an array of Bio::LiveSeq::Mutation objects
Example :
Returns : array of Mutations
Args :
See Bio::LiveSeq::Mutation for more information.
mutation¶
Title : mutation
Usage : $mutobj = $obj->mutation;
: $mutobj = $obj->mutation($objref);
Function:
Returns or sets the link-reference to the current mutation
object. If the value is not set, it will return undef.
Internal method.
Returns : an object reference or undef
DNA¶
Title : DNA
Usage : $mutobj = $obj->DNA;
: $mutobj = $obj->DNA($objref);
Function:
Returns or sets the reference to the LiveSeq object holding
the reference sequence. If there is no link, it will return
undef.
Internal method.
Returns : an object reference or undef
RNA¶
Title : RNA
Usage : $mutobj = $obj->RNA;
: $mutobj = $obj->RNA($objref);
Function:
Returns or sets the reference to the LiveSeq object holding
the reference sequence. If the value is not set, it will return
undef.
Internal method.
Returns : an object reference or undef
dnamut¶
Title : dnamut
Usage : $mutobj = $obj->dnamut;
: $mutobj = $obj->dnamut($objref);
Function:
Returns or sets the reference to the current DNAMutation object.
If the value is not set, it will return undef.
Internal method.
Returns : a Bio::Variation::DNAMutation object or undef
See Bio::Variation::DNAMutation for more information.
rnachange¶
Title : rnachange
Usage : $mutobj = $obj->rnachange;
: $mutobj = $obj->rnachange($objref);
Function:
Returns or sets the reference to the current RNAChange object.
If the value is not set, it will return undef.
Internal method.
Returns : a Bio::Variation::RNAChange object or undef
See Bio::Variation::RNAChange for more information.
aachange¶
Title : aachange
Usage : $mutobj = $obj->aachange;
: $mutobj = $obj->aachange($objref);
Function:
Returns or sets the reference to the current AAChange object.
If the value is not set, it will return undef.
Internal method.
Returns : a Bio::Variation::AAChange object or undef
See Bio::Variation::AAChange for more information.
exons¶
Title : exons
Usage : $mutobj = $obj->exons;
: $mutobj = $obj->exons($objref);
Function:
Returns or sets the reference to a current array of Exons.
If the value is not set, it will return undef.
Internal method.
Returns : an array of Bio::LiveSeq::Exon objects or undef
See Bio::LiveSeq::Exon for more information.
change_gene_with_alignment¶
Title : change_gene_with_alignment
Usage : $results=$mutate->change_gene_with_alignment($aln);
Function:
Returns a Bio::Variation::SeqDiff object containing the
results of the changes in the alignment. The alignment has
to be pairwise and have one sequence named 'QUERY', the
other one is assumed to be a part of the sequence from
$gene.
This method offers a shortcut to change_gene and
automates the creation of Bio::LiveSeq::Mutation objects.
Use it with almost identical sequnces, e.g. to locate a SNP.
Args : Bio::SimpleAlign object representing a short local alignment
Returns : Bio::Variation::SeqDiff object or 0 on error
See Bio::LiveSeq::Mutation, Bio::SimpleAlign, and Bio::Variation::SeqDiff for
more information.
create_mutation¶
Title : create_mutation
Usage :
Function:
Formats sequence differences from two sequences into
Bio::LiveSeq::Mutation objects which can be applied to a
gene.
To keep it generic, sequence arguments need not to be
Bio::LocatableSeq. Coordinate change to parent sequence
numbering needs to be done by the calling code.
Called from change_gene_with_alignment
Args : Bio::PrimarySeqI inheriting object for the reference sequence
Bio::PrimarySeqI inheriting object for the query sequence
integer for the start position of the local sequence difference
integer for the length of the sequence difference
Returns : Bio::LiveSeq::Mutation object
change_gene¶
Title : change_gene
Usage : my $mutate = Bio::LiveSeq::Mutator->new(-gene => $gene,
numbering => "coding"
);
# $mut is Bio::LiveSeq::Mutation object
$mutate->add_Mutation($mut);
my $results=$mutate->change_gene();
Function:
Returns a Bio::Variation::SeqDiff object containing the
results of the changes performed according to the
instructions present in Mutation(s). The -numbering
argument decides what molecule is being changed and what
numbering scheme being used:
-numbering => "entry"
determines the DNA level, using the numbering from the
beginning of the sequence
-numbering => "coding"
determines the RNA level, using the numbering from the
beginning of the 1st transcript
Alternative transcripts can be used by specifying
"coding 2" or "coding 3" ...
-numbering => "gene"
determines the DNA level, using the numbering from the
beginning of the 1st transcript and inluding introns.
The meaning equals 'coding' if the reference molecule
is cDNA.
Args : Bio::LiveSeq::Gene object
Bio::LiveSeq::Mutation object(s)
string specifying a numbering scheme (defaults to 'coding')
Returns : Bio::Variation::SeqDiff object or 0 on error
_mutationpos2label¶
Title : _mutationpos2label
Usage :
Function: converts mutation positions into labels
Example :
Returns : number of valid mutations
Args : LiveSeq sequence object
_set_DNAMutation¶
Title : _set_DNAMutation
Usage :
Function:
Stores DNA level mutation attributes before mutation into
Bio::Variation::DNAMutation object. Links it to SeqDiff
object.
Example :
Returns : Bio::Variation::DNAMutation object
Args : Bio::Variation::SeqDiff object
See Bio::Variation::DNAMutation and Bio::Variation::SeqDiff.
_set_effects¶
Title : _set_effects
Usage :
Function:
Stores RNA and AA level mutation attributes before mutation
into Bio::Variation::RNAChange and
Bio::Variation::AAChange objects. Links them to
SeqDiff object.
Example :
Returns :
Args : Bio::Variation::SeqDiff object
Bio::Variation::DNAMutation object
See Bio::Variation::RNAChange, Bio::Variation::RNAChange,
Bio::Variation::SeqDiff, and Bio::Variation::DNAMutation.
_untranslated¶
Title : _untranslated
Usage :
Function:
Stores RNA change attributes before mutation
into Bio::Variation::RNAChange object. Links it to
SeqDiff object.
Example :
Returns :
Args : Bio::Variation::SeqDiff object
Bio::Variation::DNAMutation object
See Bio::Variation::RNAChange, Bio::Variation::SeqDiff and
Bio::Variation::DNAMutation for details.