oligo.design.Tiled¶

class oligo.design.Tiled(genome, fa, config_path, blat=False)[source]¶

Bases: Tools, FragmentMixin

Designs oligos adjacent to each other or on adjacent fragments

Parameters:

Attributes:

blatbool: Check off-target binding using BLAT instead of STAR (not recommended for large designs), default = False
fastastr: Name of fasta file for oligo sequences, default = oligo_seqs.fa
oligo_seqsdict: Contains all oligo sequences after generating oligos

Methods

`align_to_genome`([s_idx])	Aligns oligos to the genome using BLAT or STAR
`calculate_density`([sam, blat_file])	Calculates the repeat scores and off-target binding for each oligo based on their scores from RepeatMasker and STAR/BLAT.
`detect_repeats`()	Detects repeat sequences in oligos, using RepeatMasker
`extract_repeats`()	Extracts information of repeat content from RepeatMasker output file for every oligo
`gen_oligos_capture`(chrom[, region, enzyme, ...])	Designs oligos for multiple adjacent restriction fragments across a specified region of a chromosome, or for the entire chromosome.
`gen_oligos_contig`(chrom[, region, step, oligo])	Designs adjacent oligos based on a user-defined step size, across a specified region of a chromosome, or for the entire chromosome.
`write_fasta`()	Writes oligo_seqs attribute to fasta file
`write_oligo_info`()	Writes oligo stats to oligo_info.txt

gen_oligos_capture(chrom, region='', enzyme='DpnII', oligo=70)[source]¶

Designs oligos for multiple adjacent restriction fragments across a specified region of a chromosome, or for the entire chromosome.

Parameters:

chromstr: Chromosome number/letter e.g. 7 or X
regionstr, optional: The region of the chromosome to design oligos, e.g. 10000-20000; omit this option to design oligos over the entire chromosome
enzyme{‘DpnII’, ‘NlaIII’, ‘HindIII’}, optional: The enzyme for digestion, default=DpnII
oligoint, optional: The length of the oligos to design (bp), default=70

Returns:

gen_oligos_contig(chrom, region='', step=70, oligo=70)[source]¶

Designs adjacent oligos based on a user-defined step size, across a specified region of a chromosome, or for the entire chromosome.

Parameters:

chromstr: Chromosome number/letter e.g. 7 or X
regionstr, optional: The region of the chromosome to design oligos, e.g. 10000-20000; omit this option to design oligos over the
stepint, optional: The step size, or how close adjacent oligos should be, default=70; for end-to-end oligos, set step to equal oligo
oligoint, optional: The length of the oligos to design (bp), default=70

Returns:

Raises:

oligo