Luis M Rodríguez-R
and 1 contributors

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

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