guido.off_targets
Module Contents
Functions
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Calculate sum score for a list of off-targets. |
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Get a string representation of a list of off-targets. |
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Calculate CFD score for a guide and a list of off-targets. |
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Parse mismatches from bowtie output. |
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Run bowtie to find off-targets for a list of guides. |
- guido.off_targets.calculate_ot_sum_score(off_targets, ot_mismatch_weights=[10, 5, 4, 3, 1], pam='NGG')[source]
Calculate sum score for a list of off-targets.
- guido.off_targets.get_off_targets_string(off_targets, pam='NGG')[source]
Get a string representation of a list of off-targets.
- guido.off_targets.calculate_cfd_score(guide, offtargets, mm_scores, pam_scores)[source]
Calculate CFD score for a guide and a list of off-targets.
Adapted from Doench et al. 2016, https://doi.org/10.1038/nbt.3437
- guido.off_targets._parse_mismatches(mismatches, strand, seq_len)[source]
Parse mismatches from bowtie output.
Returns a dictionary with mismatches positions as keys and mismatched nucleotides as values.
- guido.off_targets.run_bowtie(guides, pam='NGG', core_length=10, core_mismatches=2, total_mismatches=4, genome_index_path=None, threads=1, bowtie_path='bin/bowtie/')[source]
Run bowtie to find off-targets for a list of guides.
# TODO: add description of mismatch settings
- Parameters:
- guidesGuide[]
List of guides to find off-targets for.
- pamstr, optional
PAM sequence, by default “NGG”
- core_lengthint, optional
gRNA core length, by default 10
- core_mismatchesint, optional
Allowed mismatches in core gRNA sequence, by default 2
- total_mismatchesint, optional
Total allowed mismatches. Max 4, by default 4
- genome_index_pathGenome, optional
Genome object to search off-targets in, by default None
- threadsint, optional
Number of threads to run bowtie with, by default 1
- bowtie_pathstr, optional
Path to bowtie binary, by default “bin/bowtie/”
- Returns:
- list
List of off-targets for each guide.