Bio::LiveSeq::Transcript(3pm) User Contributed Perl Documentation Bio::LiveSeq::Transcript(3pm)NAME
Bio::LiveSeq::Transcript - Transcript class for LiveSeq
SYNOPSIS
# documentation needed
DESCRIPTION
This stores information about coding sequences (CDS). The implementation is that a Transcript object accesses a collection of Exon
objects, inferring from them the nucleotide structure and sequence.
AUTHOR - Joseph A.L. Insana
Email: 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 _
new
Title : new
Usage : $transcript = Bio::LiveSeq::Transcript->new(-exons => @obj_refs);
Function: generates a new Bio::LiveSeq::Transcript
Returns : reference to a new object of class Transcript
Errorcode -1
Args : reference to an array of Exon object references
all_Exons
Title : all_Exons
Usage : $transcript_obj->all_Exons()
Function: returns references to all Exon objects the Transcript is composed of
Example : foreach $exon ($transcript->all_Exons()) { do_something }
Returns : array of object references
Args : none
downstream_seq
Title : downstream_seq
Usage : $transcript_obj->downstream_seq()
: $transcript_obj->downstream_seq(64)
Function: returns a string of nucleotides downstream of the end of the
CDS. If there is some information of the real mRNA, from features in
an attached Gene object, it will return up to those boundaries.
Otherwise it will return 1000 nucleotides.
If an argument is given it will override the default 1000 number
and return instead /that/ requested number of nucleotides.
But if a Gene object is attached, this argument will be ignored.
Returns : string
Args : an optional integer number of nucleotides to be returned instead of
the default if no gene attached
upstream_seq
Title : upstream_seq
Usage : $transcript_obj->upstream_seq()
: $transcript_obj->upstream_seq(64)
Function: just like downstream_seq but returns nucleotides before the ATG
Note : the default, if no Gene information present and no nucleotides
number given, is to return up to 400 nucleotides.
get_Translation
Title : valid
Usage : $translation = $obj->get_Translation()
Function: retrieves the reference to the object of class Translation (if any)
attached to a LiveSeq object
Returns : object reference
Args : none
translation_table
Title : translation_table
Usage : $name = $obj->translation_table;
: $name = $obj->translation_table(11);
Function: Returns or sets the translation_table used for translating the
transcript.
If it has never been set, it will return undef.
Returns : an integer
frame
Title : frame
Usage : $frame = $transcript->frame($label);
Function: Returns the frame of a particular nucleotide.
Frame can be 0 1 or 2 and means the position in the codon triplet
of the particulat nucleotide. 0 is the first codon_position.
Codon_position (1 2 3) is simply frame+1.
If the label asked for is not inside the Transcript, -1 will be
returned.
Args : a label
Returns : 0 1 or 2
Errorcode -1
perl v5.14.2 2012-03-02 Bio::LiveSeq::Transcript(3pm)
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Bio::LiveSeq::Mutator(3pm) User Contributed Perl Documentation Bio::LiveSeq::Mutator(3pm)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://redmine.open-bio.org/projects/bioperl/
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.
perl v5.14.2 2012-03-02 Bio::LiveSeq::Mutator(3pm)