/ 
PrimerMap-1.3
River stage zero No dependents
/ PrimerMap

NAME

PrimerMap - generates a primer sequence graphical map

SYNOPSIS

use PrimerMap;
use Data::Dumper;

my $start  = "12,24,28,32,824,888,902";
my $end    = "40,59,48,50,801,848,880";
my $output = "myGene.png";

# can also collect primer coordinates from a text file 
# my $inFile = "primermap_file.txt";
# $tmp->read_file($inFile);

my $tmp = PrimerMap->new();
$tmp->load_map(
   primer_start => $start,
   primer_end   => $end,
   seq_length   => "1200",
   gene_name    => "myGene",
   out_file     => $output || "output.png"
);

# take a look at the object 
print Dumper($tmp);

# print the primer map
$tmp->primer_map();
print "\n\n";

# getters and setters can be used as follows:
my $set_start = $tmp->set_start("22,24,2226");
print $set_start. "\n\n";

my $get_start = $tmp->get_start();
print $get_start. "\n\n";

my $set_end = $tmp->set_end("52,64,2202");
print $set_end. "\n\n";

my $get_end = $tmp->get_end();
print $get_end. "\n\n";

my $set_length = $tmp->set_length(2500);
print $set_length. "\n\n";

my $get_length = $tmp->get_length();
print $get_length. "\n\n";

my $set_id = $tmp->set_ID("myNewGeneName");
print $set_id. "\n\n";

my $get_id = $tmp->get_ID();
print $get_id. "\n\n";

my $set_file = $tmp->set_outfile("myOutPutFile.png");
print $set_file. "\n\n";

my $get_file = $tmp->get_outfile();
print $get_file. "\n\n";

# see the newly set object
print Dumper($tmp);

# see the newly set primer map
$tmp->primer_map();
print "\n\n";

DESCRIPTION

This object extends the Bio::SeqFeature::Generic class to provide an object for Bio::Graphics. Uses primer starting and ending coordinates (base pairs) to generate a primer map relative to a base sequence.

FEEDBACK

damienoh@gwu.edu

Mailing Lists

User feedback is an integral part of the evolution of this module. Send your comments and suggestions preferably to one of the mailing lists. Your participation is much appreciated.

Support

Please direct usage questions or support issues to: <damienoh@gwu.edu> Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the GitHub bug tracking system to help keep track of the bugs and their resolution. Bug reports can be submitted via the GitHub page:

https://github.com/dohalloran/Bio-SeqFeature-Generic-Ext-PrimerMap/issues

AUTHORS - Damien OHalloran

Email: damienoh@gwu.edu

APPENDIX

The rest of the documentation details each of the object methods.

read_file()

Title   : read_file()
Usage   : my $tmp->read_file($inFile);
Function: get data for $self hash from a file
Returns : Populates the $self->{start} and $self->{end} properties
Args    : $filename, a texfile that contains input data of primer 
starting and ending features as base pairs e.g.: 
12,24,28,32,824,888,902
40,59,48,50,801,848,880
note: the starting positions is the first line

load_map()

Title   : load_map()
Usage   : my $tmp->load_map(
           primer_start => $start, #don't include if loading file
           primer_end   => $end, #don't include if loading file
           seq_length   => "1200",
           gene_name    => "myGene",
           out_file     => $output || "output.png"
           );
Function: Populates the user data into $self hash
Returns : nothing returned
Args    : 
-primer_start, a csv string of starting base pairs for primers
-primer_end, a csv string of final base pairs for primers
-seq_length, the length in base pairs of the gene sequence
-gene_name, the ID to give to the gene (optional)
-out_file, name of the resulting graphical output file (optional)

get_start()

Title   : get_start()
Usage   : my $get_start = $tmp->get_start();
Function: Retrieves the primer starting features
Returns : A string containing primer start features
Args    : none

set_start()

Title   : set_start()
Usage   : my $set_start = $tmp->set_start("22,24,2226");
Function: Populates the $self->{start} property
Returns : $self->{start}
Args    : a csv string of starting base pairs for primers

get_end()

Title   : get_end()
Usage   : my $get_end = $tmp->get_end();
Function: Retrieves the primer ending features
Returns : A string containing primer end features
Args    : none

set_end()

Title   : set_end()
Usage   : my $set_end = $tmp->set_end("52,64,2202");
Function: Populates the $self->{end} property
Returns : $self->{end}
Args    : a csv string of ending base pairs for primers

get_ID()

Title   : get_ID()
Usage   : my $get_ID = $tmp->get_ID();
Function: Retrieves the gene name
Returns : A string containing gene name 
Args    : none

set_ID()

Title   : set_ID()
Usage   : my $set_id = $tmp->set_ID("myNewGeneName");
Function: Populates the $self->{seq_id} property
Returns : $self->{seq_id}
Args    : the ID to give to the gene

get_outfile()

Title   : get_outfile()
Usage   : my $get_outfile = $tmp->get_outfile();
Function: Retrieves the output filename
Returns : A string containing filename
Args    : none

set_outfile()

Title   : set_outfile()
Usage   : my $set_output = $tmp->set_outfile("myOutPutFile.txt");
Function: Populates the $self->{out_file} property
Returns : $self->{out_file}
Args    : name of the resulting graphical output file

get_length()

Title   : get_length()
Usage   : my $get_length = $tmp->get_length();
Function: Retrieves the sequence length in base pairs
Returns : Gene length
Args    : none

set_length()

Title   : set_length()
Usage   : my $set_length = $tmp->set_length(2500);
Function: Populates the $self->{seq_len} property
Returns : $self->{seq_len}
Args    : length of gene

primer_map()

Title   : primer_map()
Usage   : my $tmp->primer_map();
Function: Populate the panels for Bio::Graphics::Panel and Bio::SeqFeature::Generic
Returns : A graphical files containing primer sequence map
Args    : all collected from the Bio::SeqFeature::Generic constructor

LICENSE AND COPYRIGHT

Copyright (C) 2016 Damien M. O'Halloran
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991