SlideMap 1.2.2

SlideMap is a Perl module for the creation of MicroArray slide maps.

SYNOPSIS

 use SlideMap;
 
 $sm = SlideMap->new( machine => "arrayer", x_pin => 2, y_pin => 6,
 xspacing => 0, yspacing => 0, x_repeat => 1,
 y_repeat => 1);
 
 $sm->initialize;
 $sm->fill_map;
 $map_ref = $sm->getMap;
 
 ($array_row, $array_col, $meta_row, $meta_col, $sub_row, $sub_col)
 = $sm->convert_well($plate_num, $well);
 
 ($plate_num, $well, $plate_row, $plate_col)
 = $sm->convert_spot($array_row, $array_col);

 ($_meta_row,$_meta_col,$_sub_row,$_sub_col)
 = $sm->get_meta($array_row, $array_col);
 
 $sm->setMachine("arrayer");
 $arrayer = $sm->getMachine;
 
 $sm->setPrintHead(2, 6);
 ($x_pin, $y_pin) = $sm->getPrintHead;
 
 $sm->setBlockDimensions(25, 24);
 ($x_spacing, $y_spacing) = $sm->getBlockDimensions;
 
 $sm->setNoComplement([ 0 | 1 ]);
 $noComplement = $sm->getNoComplement;
 
 $sm->setRepeats([ 1 | 2 | 3 | 4 ], [ 1 | 2 | 3 | 4 ]);
 ($x_repeat,$y_repeat) = $sm->getRepeatMode;

 $sm->setRepeatMode([ 0 | 1 ]);
 $repeatMode = $sm->getRepeatMode;
 
 $sm->setFormat([ 1 | 2 ]);
 $plate_format = $sm->getFormat;
 
 $sm->setPrintDirection([ 0 | 1 ]);
 $direction = $sm->getPrintDirection;
 
 $sm->setPlateOrder("[A,B,C,D,E,F,G ... | 1,2,3,4,5, ... ]");
 $plate_order = $sm->getPlateOrder;
 
 ($max_array_row,$max_array_col) = $sm->getArrayDimensions;

 ($x_pitch,$y_pitch) = $sm->getPitch;

 $number_of_spots = $sm->getNumSpots;

 $sm->diagnostics;
 $sm->print_spots([ 1 | 0 ]);
 $sm->print_wells([ 1 | 0 ]);
 $sm->showConvertWell;
 $sm->showConvertSpot;

SlideMap is used to create a row/col -> plate/well map of a microarray slide. It does not as yet incorporate annotation data into the map, but simply creates the map object based on input parameters. The map is an ordered list of spots with references to annonymous arrays containing array_row, array_col, plate_alias, well. SlideMap currently supports 5 types of arrayers: IAS (default), MD, MD3, Lucidia, and Stanford. (Others will be implemented as needed.)

SlideMap provides 2 methods for conversion of spots->wells and vise-versa, based on instantiated parameters.

The main parameters are: machine: the type of array printing machine used (IAS is the default) x_pin: the number of print head pens in the 'X' (plate_row) dimension y_pin: the number of print head pens in the 'Y' (plate_col) dimension (x_pin = 2, and y_pin = 6 are the defaults) x_spacing: the number of spots in one row of a block on the array y_spacing: the number of spots in one column of a block on the array (x_spacing = 24, and y_spacing = 25 are the defaults) x_repeat: the number of repeated block in the 'X' dimension (default = 1) y_repeat: the number of repeated block in the 'Y' dimension (default = 1)


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· Perl