I still don't believe I am explaining it correctly:
The index number for the given data must match that of the reference.
Data:
Code:
Index Chr Genotype Mutation Type
1 Chr1 TT Intronic
2 Chr1 AA Exonic
3 Chr1 AG Exonic
4 Chr1 CC Frameshift
5 Chr1 CA Intronic
Reference:
Code:
1)T
2)A
3)C
4)G
5)C
For example: The genotype at position 1 is TT and the reference is T. Because atleast one of the letters in the genotype matches the reference, then the program should move on.
At position 3, the genotype is AG and the reference is C. Neither of the letters that make up the genotype match the reference, so the program should take note of this and display '3 Chr1 AG Exonic' in the output.
Thanks again
Moderator's Comments:
edit by bakunin: please use [CODE]..[/CODE]-tags ehen posting code or file content. It makes it easier to read and it stays formatted. Thank you.
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LEARN ABOUT DEBIAN
bio::popgen::genotypei
Bio::PopGen::GenotypeI(3pm) User Contributed Perl Documentation Bio::PopGen::GenotypeI(3pm)NAME
Bio::PopGen::GenotypeI - A marker and alleles for a specific individual
SYNOPSIS
Give standard usage here
DESCRIPTION
Describe the interface here
FEEDBACK
Mailing Lists
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 list. 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 of the bugs and their resolution. Bug reports can be submitted via
email or the web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
marker_name
Title : marker_name
Usage : my $name = $genotype->marker_name();
Function: Get the marker name for a genotype result
Returns : string
Args : none
individual_id
Title : individual_id
Usage : my $indid = $genotype->individual_id();
Function: Gets the individual id associated with a genotype
This is effectively a back reference since we will typically
associate a genotype with an individual with an
individual HAS-A genotype relationship.
Returns : unique id string for an individual
Args : none
annotation
Title : annotation
Usage : my $annotation_collection = $genotype->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this genotype
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
get_Alleles
Title : get_Alleles
Usage : my @alleles = $genotype->get_Alleles();
Function: Get the alleles for a given marker and individual
Returns : array of alleles (strings in many implementations)
Args : none
perl v5.14.2 2012-03-02 Bio::PopGen::GenotypeI(3pm)
06-06-2012
