oligo.design.Capture

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

Bases: Tools, FragmentMixin

Designs oligos for Capture-C

Parameters:
genome{‘mm9’, ‘mm10’, ‘hg18’, ‘hg19’, ‘hg38’}

Genome build

fastr

Path to reference genome fasta

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(bed[, enzyme, oligo])

Generates oligos flanking restriction fragments that encompass the coordinates supplied in the bed file

write_fasta()

Writes oligo_seqs attribute to fasta file

write_oligo_info()

Writes oligo stats to oligo_info.txt

gen_oligos(bed, enzyme='DpnII', oligo=70)[source]

Generates oligos flanking restriction fragments that encompass the coordinates supplied in the bed file

Parameters:
bedstr

Path to tab-delimited bed file containing a list of coordinates for viewpoints in the capture experiment. Must be in the format ‘chr’\t’start’\t’stop’\t’name’\n

enzyme{‘DpnII’, ‘NlaIII’, ‘HindIII’}, optional

The enzyme for digestion, default = DpnII

oligoint, optional

The length of the oligo to design (bp), default = 70

Returns:
selfobject