NAME

Bio::Polloc::Locus::crispr - A CRISPR locus

DESCRIPTION

A CRISPR locus. Implements Bio::Polloc::LocusI.

AUTHOR - Luis M. Rodriguez-R

Email lmrodriguezr at gmail dot com

APPENDIX

Methods provided by the package

new

• Creates a Bio::Polloc::Locus::repeat object.

• Arguments

  -spacers_no int

  The number of spacers.

  -dr str

  Direct repeat sequence.

spacers_no

• Gets/sets the number of spacers.

• Arguments

  The number of spacers (int, optional).

• Returns

  The number of spacers (int or undef).

dr

• Sets/gets the Direct Repeat sequence.

• Arguments

  The direct repeat sequence (str, optional).

• Returns

  The direct repeat sequence (str or undef).

score

• Gets/sets the score.

• Arguments

  The score (float, optional).

• Returns

  The score (float or undef).

add_spacer

• Adds information for an spacer.

• Arguments

  -from int

  Where the spacer starts. This is a coordinate on the whole genome (or defined global sequence), NOT with respect to the CRISPR.

  -to int

  Where the spacer ends. This is a coordinate on the whole genome (or defined global sequence). NOT with respect to the CRISPR.

  -raw_seq str

  Optional parameter to set the raw sequence of the spacer. If not provided, it is calculated based on the coordinates. If no global sequence is set, it remains undefined.

spacers

• Gets the spacers as an arrayref or hashrefs with keys from, to and raw_seq.

repeats

• Gets the repeats as an arrayref of hashrefs with keys from and to. The actual sequence of the repeats can be retrieved using dr. There is no way to directly set the coordinates of the repeats, instead, you must set the coordinates of the spacers.

INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

_initialize