| Bio::Variation::AAReverseMutate(3pm) | User Contributed Perl Documentation | Bio::Variation::AAReverseMutate(3pm) |
Bio::Variation::AAReverseMutate - point mutation and codon
information from single amino acid changes
$aamut = Bio::Variation::AAReverseMutate->new
(-aa_ori => 'F',
-aa_mut => 'S',
-codon_ori => 'ttc', # optional
-codon_table => '3' # defaults to 1
);
@points = $aamut->each_Variant;
if (scalar @points > 0 ) {
foreach $rnachange ( @points ) {
# $rnachange is a Bio::Variation::RNAChange object
print " ", $rnachange->allele_ori->seq, ">",
$rnachange->allele_mut->seq, " in ",
$rnachange->codon_ori, ">", $rnachange->codon_mut,
" at position ", $rnachange->codon_pos, "\n";
}
} else {
print "No point mutations possible\n",
}
Bio::Variation::AAReverseMutate objects take in reference and mutated amino acid information and deduces potential point mutations at RNA level leading to this change. The choice can be further limited by letting the object know what is the the codon in the reference sequence. The results are returned as Bio::Variation::RNAChange objects.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : aa_ori
Usage : $obj->aa_ori();
Function:
Sets and returns original aa sequence. If value is not
set, returns false.
Amino acid sequences are stored in upper case characters,
others in lower case.
Example :
Returns : string
Args : single character amino acid code
Title : aa_mut
Usage : $obj->aa_mut();
Function:
Sets and returns the mutated allele sequence. If value is not
set, returns false.
Example :
Returns : string
Args : single character amino acid code
Title : codon_ori
Usage : $obj->codon_ori();
Function:
Sets and returns codon_ori triplet. If value is not set,
returns false. The string has to be three characters
long. The character content is not checked.
Example :
Returns : string
Args : string
Title : codon_table
Usage : $obj->codon_table();
Function:
Sets and returns the codon table id of the RNA
If value is not set, returns 1, 'universal' code, as the default.
Example :
Returns : integer
Args : none if get, the new value if set
Title : each_Variant
Usage : $obj->each_Variant();
Function:
Returns a list of Variants.
Example :
Returns : list of Variants
Args : none
| 2021-12-02 | perl v5.32.1 |