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