beditor
(v2)
A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more
Usage
🖱️ GUI-mode
beditor gui
Note: GUI is recommended for designing small libraries and prioritization of the guides.
▶️ CLI-mode
beditor cli --editor BE1 -m path/to/mutations.tsv -o path/to/output_directory/ --species human --ensembl-release 110
or
beditor cli -c beditor_config.yml
Parameters
usage: beditor cli [--editor EDITOR] [-m MUTATIONS_PATH] [-o OUTPUT_DIR_PATH]
[--species SPECIES] [--ensembl-release ENSEMBL_RELEASE]
[--genome-path GENOME_PATH] [--gtf-path GTF_PATH] [-r RNA_PATH] [-p PRT_PATH]
[-c CONFIG_PATH]
[--search-window SEARCH_WINDOW] [-n]
[-w WD_PATH] [-t THREADS] [-k KERNEL_NAME] [-v VERBOSE] [-i IGV_PATH_PREFIX] [--ext EXT] [-f] [-d] [--skip SKIP]
optional arguments:
-h, --help show this help message and exit
--editor EDITOR base-editing method, available methods can be listed using command: 'beditor resources'
-m MUTATIONS_PATH, --mutations-path MUTATIONS_PATH
path to the mutation file, the format of which is available at https://github.com/rraadd88/beditor/README.md#Input-format.
-o OUTPUT_DIR_PATH, --output-dir-path OUTPUT_DIR_PATH
path to the directory where the outputs should be saved.
--species SPECIES species name.
--ensembl-release ENSEMBL_RELEASE
ensemble release number.
--genome-path GENOME_PATH
path to the genome file, which is not available on Ensembl.
--gtf-path GTF_PATH path to the gene annotations file, which is not available on Ensembl.
-r RNA_PATH, --rna-path RNA_PATH
path to the transcript sequences file, which is not available on Ensembl.
-p PRT_PATH, --prt-path PRT_PATH
path to the protein sequences file, which is not available on Ensembl.
--search-window SEARCH_WINDOW
number of bases to search on either side of a target, if not specified, it is inferred by beditor.
-n, --not-be False
do not process as a base editor.
-c CONFIG_PATH, --config-path CONFIG_PATH
path to the configuration file.
-w WD_PATH, --wd-path WD_PATH
path to the working directory.
-t THREADS, --threads THREADS
1
number of threads for parallel processing.
-k KERNEL_NAME, --kernel-name KERNEL_NAME
'beditor'
name of the jupyter kernel.
-v VERBOSE, --verbose VERBOSE
'WARNING'
verbose, logging levels: DEBUG > INFO > WARNING > ERROR (default) > CRITICAL.
-i IGV_PATH_PREFIX, --igv-path-prefix IGV_PATH_PREFIX
prefix to be added to the IGV URL.
--ext EXT file extensions of the output tables.
-f, --force False
-d, --dbug False
--skip SKIP skip sections of the workflow
Examples:
Notes:
Required parameters for assigning a species:
species
ensembl_release
or
genome_path
gtf_path
rna_path
prt_path
Installation
Virtual environment and namming kernel (recommended)
conda env create -n beditor python=3.9; # options: conda/mamba, python=3.9/3.8
python -m ipykernel install --user --name beditor
Installation of the package
pip install beditor[all]
Optional dependencies, as required:
pip install beditor # only cli
pip install beditor[gui] # plus gui
For fast processing of large genomes (highly recommended for human genome):
conda install install bioconda::ucsc-fatotwobit bioconda::ucsc-twobittofa bioconda::ucsc-twobitinfo # options: conda/mamba
Else, for moderately fast processing,
conda install install bioconda::bedtools # options: conda/mamba
Input format
Note: The coordinates are 1-based (i.e. X:1-1
instead of X:0:1
) and IDs correspond to the chosen genome assemblies (e.g. from Ensembl).
Point mutations
chrom start end strand mutation
5 1123 1123 + C
Position scanning
chrom start end strand
5 1123 1123 +
Region scanning
chrom start end strand
5 1123 2123 +
Protein point mutations
protein id aa pos mutation
ENSP1123 43 S
Protein position scanning
protein id aa pos
ENSP1123 43
Protein region scanning
protein id aa start aa end
ENSP1123 43 143
Note: Ensembl protein IDs are used.
Output format
Note: output contains 0-based coordinates are used.
guide sequence guide locus offtargets score {columns in the input}
AGCGTTTGGCAAATCAAACAAAA 4:1003215-1003238(+) 0 1 ..
Supported base editing methods
method | nucleotide | nucleotide mutation | window start | window end | guide length | PAM | PAM position |
---|---|---|---|---|---|---|---|
A3A-BE3 | C | T | 4 | 8 | 20 | NGG | down |
ABE7.10 | A | G | 4 | 7 | 20 | NGG | down |
ABE7.10* | A | G | 4 | 8 | 20 | NGG | down |
ABE7.9 | A | G | 5 | 8 | 20 | NGG | down |
ABESa | A | G | 6 | 12 | 21 | NNGRRT | down |
BE-PLUS | C | T | 4 | 14 | 20 | NGG | down |
BE1 | C | T | 4 | 8 | 20 | NGG | down |
BE2 | C | T | 4 | 8 | 20 | NGG | down |
BE3 | C | T | 4 | 8 | 20 | NGG | down |
BE4-Gam | C | T | 4 | 8 | 20 | NGG | down |
BE4/BE4max | C | T | 4 | 8 | 20 | NGG | down |
Cas12a-BE | C | T | 10 | 12 | 23 | TTTV | up |
eA3A-BE3 | C | T | 4 | 8 | 20 | NGG | down |
EE-BE3 | C | T | 5 | 6 | 20 | NGG | down |
HF-BE3 | C | T | 4 | 8 | 20 | NGG | down |
Sa(KKH)-ABE | A | G | 6 | 12 | 21 | NNNRRT | down |
SA(KKH)-BE3 | C | T | 3 | 12 | 21 | NNNRRT | down |
SaBE3 | C | T | 3 | 12 | 21 | NNGRRT | down |
SaBE4 | C | T | 3 | 12 | 21 | NNGRRT | down |
SaBE4-Gam | C | T | 3 | 12 | 21 | NNGRRT | down |
Target-AID | C | T | 2 | 4 | 20 | NGG | down |
Target-AID | C | T | 2 | 4 | 20 | NG | down |
VQR-ABE | A | G | 4 | 6 | 20 | NGA | down |
VQR-BE3 | C | T | 4 | 11 | 20 | NGAN | down |
VRER-ABE | A | G | 4 | 6 | 20 | NGCG | down |
VRER-BE3 | C | T | 3 | 10 | 20 | NGCG | down |
xBE3 | C | T | 4 | 8 | 20 | NG | down |
YE1-BE3 | C | T | 5 | 7 | 20 | NGG | down |
YE2-BE3 | C | T | 5 | 6 | 20 | NGG | down |
YEE-BE3 | C | T | 5 | 6 | 20 | NGG | down |
Favorite base editor not listed?
Please send the required info using a PR, or an issue.
Change log
v2
New features:
- Design libraries for base or amino acid mutational scanning, at defined positions and regions.
- The
gui
contains library filtering and prioritization options. - Non-base editing applications, e.g. CRISPR-tiling, using
not_be
option.
Key updates:
- Quicker installation due to reduced number of dependencies (
bwa
comes in the package, andsamtools
not needed). - Faster run-time, compared to v1, because of the improvements in the dependencies e.g.
pandas
etc. - Faster run-time on large genomes e.g. human genome, because of the use of 2bit tools.
- Direct command line options to use non-model species which e.g. not indexed on Ensembl.
- Configuration made optional.
Technical updates:
- The
gui
is powered bymercury
, thus overcomming the limitations of v1. - Use of one base editor (
method
) per run, instead of multiple. - Due to overall faster run-times, parallelization within a run is disabled. However, multiple runs can be parallelized, externally e.g. using Python's built-in
multiprocessing
. - Only the sgRNAs for which target lies within the optimal activity window are reported. Therefore unneeded penalty for target not being in activity window is now not utilized, but options retained for back-compatibility.
- Many refactored functions can now be imported and executed independently for "much more" applications.
- Reports generated for each run in the form of a jupyter notebook.
- Automated testing on GitHub for continuous integration.
- The
cli
is compatible with python 3.8 and 3.9 (even higher untested versions), however thegui
not supported on python 3.7 due lack of dependencies.
Future directions, for which contributions are welcome:
- Adding option to provide 0-based co-ordinates in the input.
Similar projects:
- http://www.rgenome.net/be-designer/
- http://yang-laboratory.com/BEable-GPS
- https://github.com/maxwshen/be_predict_bystander
- https://github.com/maxwshen/be_predict_efficiency
- https://fgcz-shiny.uzh.ch/PnBDesigner/
How to cite?
v2
- Using BibTeX:
@software{Dandage_beditor,
title = {beditor: A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing},
author = {Dandage, Rohan},
year = {2024},
url = {https://doi.org/10.1534/genetics.119.302089},
version = {v2.0.0},
note = {The URL is a DOI link to the permanent archive of the software.},
}
-
Using citation information from CITATION.CFF file.
v1
- Using BibTeX:
@software{Dandage_beditorv1,
title = {beditor: A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing},
author = {Dandage, Rohan},
year = {2019},
url = {https://doi.org/10.1534/genetics.119.302089},
version = {v1},
}
Future directions, for which contributions are welcome:
- Allowing 0-based coordinates in the input.
Similar projects:
- http://www.rgenome.net/be-designer/
- http://yang-laboratory.com/BEable-GPS
- https://github.com/maxwshen/be_predict_bystander
- https://github.com/maxwshen/be_predict_efficiency
- https://fgcz-shiny.uzh.ch/PnBDesigner/
API
beditor.lib.get_mutations
module Mutation co-ordinates using pyensembl
get_protein_cds_coords
function get_protein_cds_coords(annots, protein_id: str) → DataFrame
Get protein CDS coordinates
Args:
-
annots
: pyensembl annotations -
protein_id
(str): protein ID
Returns:
-
pd.DataFrame
: output table
get_protein_mutation_coords
function get_protein_mutation_coords(data: DataFrame, aapos: int, test=False) → tuple
Get protein mutation coordinates
Args:
-
data
(pd.DataFrame): input table -
aapos
(int): amino acid position -
test
(bool, optional): test-mode. Defaults to False.
Raises:
-
ValueError
: invalid positions
Returns:
-
tuple
: aapos,start,end,seq
map_coords
function map_coords(df_: DataFrame, df1_: DataFrame, verbose: bool = False) → DataFrame
Map coordinates
Args:
-
df_
(pd.DataFrame): input table
Returns:
-
pd.DataFrame
: output table
get_mutation_coords_protein
function get_mutation_coords_protein(
df0: DataFrame,
annots,
search_window: int,
outd: str = None,
force: bool = False,
verbose: bool = False
) → DataFrame
Get mutation coordinates for protein
Args:
-
df0
(pd.DataFrame): input table -
annots
(type): pyensembl annotations -
search_window
(int): search window length on either side of the target -
outd
(str, optional): output directory path. Defaults to None. -
force
(bool, optional): force. Defaults to False. -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
pd.DataFrame
: output table
get_mutation_coords
function get_mutation_coords(
df0: DataFrame,
annots,
search_window: int,
verbose: bool = False,
**kws_protein
) → DataFrame
Get mutation coordinates
Args:
-
df0
(pd.DataFrame): input table -
annots
(type): pyensembl annotation -
search_window
(int): search window length on either side of the target -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
pd.DataFrame
: output table
beditor.lib.get_scores
module Scores
get_ppamdist
function get_ppamdist(
guide_length: int,
pam_len: int,
pam_pos: str,
ppamdist_min: int
) → DataFrame
Get penalties set based on distances of the mismatch/es from PAM
:param guide_length: length of guide sequence :param pam_len: length of PAM sequence :param pam_pos: PAM location 3' or 5' :param ppamdist_min: minimum penalty :param pmutatpam: penalty for mismatch at PAM
TODOs: Use different scoring function for different methods.
get_beditorscore_per_alignment
function get_beditorscore_per_alignment(
NM: int,
alignment: str,
pam_len: int,
pam_pos: str,
pentalty_genic: float = 0.5,
pentalty_intergenic: float = 0.9,
pentalty_dist_from_pam: float = 0.1,
verbose: bool = False
) → float
Calculates beditor score per alignment between guide and genomic DNA.
:param NM: Hamming distance :param mismatches_max: Maximum mismatches allowed in alignment :param alignment: Symbol '|' means a match, '.' means mismatch and ' ' means gap. e.g. |||||.||||||||||.||||.| :param pentalty_genic: penalty for genic alignment :param pentalty_intergenic: penalty for intergenic alignment :param pentalty_dist_from_pam: maximum pentalty for a mismatch at PAM () :returns: beditor score per alignment.
get_beditorscore_per_guide
function get_beditorscore_per_guide(
guide_seq: str,
strategy: str,
align_seqs_scores: DataFrame,
dBEs: DataFrame,
penalty_activity_window: float = 0.5,
test: bool = False
) → float
Calculates beditor score per guide.
:param guide_seq: guide seqeunce 23nts :param strategy: strategy string eg. ABE;+;@-14;ACT:GCT;T:A; :param align_seqs_scores: list of beditor scores per alignments for all the alignments between guide and genomic DNA :param penalty_activity_window: if editable base is not in activity window, penalty_activity_window=0.5 :returns: beditor score per guide.
revcom
function revcom(s)
calc_cfd
function calc_cfd(wt, sg, pam)
get_cfdscore
function get_cfdscore(wt, off)
beditor.lib.get_specificity
module Specificities
run_alignment
function run_alignment(
src_path: str,
genomep: str,
guidesfap: str,
guidessamp: str,
guidel: int,
mismatches_max: int = 2,
threads: int = 1,
force: bool = False,
verbose: bool = False
) → str
Run alignment
Args:
-
src_path
(str): source path -
genomep
(str): genome path -
guidesfap
(str): guide fasta path -
guidessamp
(str): guide sam path -
threads
(int, optional): threads. Defaults to 1. -
force
(bool, optional): force. Defaults to False. -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
str
: alignment file.
read_sam
function read_sam(align_path: str) → DataFrame
read alignment file
Args:
-
align_path
(str): path to the alignment file
Returns:
-
pd.DataFrame
: output table
Notes:
Tag Meaning NM Edit distance MD Mismatching positions/bases AS Alignment score BC Barcode sequence X0 Number of best hits X1 Number of suboptimal hits found by BWA XN Number of ambiguous bases in the referenece XM Number of mismatches in the alignment XO Number of gap opens XG Number of gap extentions XT Type: Unique/Repeat/N/Mate-sw XA Alternative hits; format: (chr,pos,CIGAR,NM;)* XS Suboptimal alignment score XF Support from forward/reverse alignment XE Number of supporting seeds Reference: https://bio-bwa.sourceforge.net/bwa.shtml
parse_XA
function parse_XA(XA: str) → DataFrame
Parse XA tags
Args:
-
XA
(str): XA tag
Notes:
format: (chr,pos,CIGAR,NM;)
Example: XA='4,+908051,23M,0;4,+302823,23M,0;4,-183556,23M,0;4,+1274932,23M,0;4,+207765,23M,0;4,+456906,23M,0;4,-1260135,23M,0;4,+454215,23M,0;4,-1177442,23M,0;4,+955254,23M,1;4,+1167921,23M,1;4,-613257,23M,1;4,+857893,23M,1;4,-932678,23M,2;4,-53825,23M,2;4,+306783,23M,2;'
get_extra_alignments
function get_extra_alignments(
df1: DataFrame,
genome: str,
bed_path: str,
alignments_max: int = 10,
threads: int = 1
) → DataFrame
Get extra alignments
Args:
-
df1
(pd.DataFrame): input table -
alignments_max
(int, optional): alignments max. Defaults to 10. -
threads
(int, optional): threads. Defaults to 1.
Returns:
-
pd.DataFrame
: output table
TODOs: 1. apply parallel processing to get_seq
to_pam_coord
function to_pam_coord(
pam_pos: str,
pam_len: int,
align_start: int,
align_end: int,
strand: str
) → tuple
Get PAM coords
Args:
-
pam_pos
(str): PAM position -
pam_len
(int): PAM length -
align_start
(int): alignment start -
align_end
(int): alignment end -
strand
(str): strand
Returns:
-
tuple
: start,end
get_alignments
function get_alignments(
align_path: str,
genome: str,
alignments_max: int,
pam_pos: str,
pam_len: int,
guide_len: int,
pam_pattern: str,
pam_bed_path: str,
extra_bed_path: str,
**kws_xa
) → DataFrame
Get alignments
Args:
-
align_path
(str): alignement path -
genome
(str): genome path -
pam_pos
(str): PAM position -
pam_len
(int): PAM length -
guide_len
(int): sgRNA length -
pam_pattern
(str): PAM pattern -
pam_bed_path
(str): PAM bed path
Returns:
-
pd.DataFrame
: output path
get_penalties
function get_penalties(
aligns: DataFrame,
guides: DataFrame,
annots: DataFrame
) → DataFrame
Get penalties
Args:
-
aligns
(pd.DataFrame): alignements -
guides
(pd.DataFrame): guides -
annots
(pd.DataFrame): annotations
Returns:
-
pd.DataFrame
: output table
score_alignments
function score_alignments(
df4: DataFrame,
pam_len: int,
pam_pos: str,
pentalty_genic: float = 0.5,
pentalty_intergenic: float = 0.9,
pentalty_dist_from_pam: float = 0.1,
verbose: bool = False
) → tuple
score_alignments summary
Args:
-
df4
(pd.DataFrame): input table -
pam_pos
(str): PAM position -
pentalty_genic
(float, optional): penalty for offtarget in genic locus. Defaults to 0.5. -
pentalty_intergenic
(float, optional): penalty for offtarget in intergenic locus. Defaults to 0.9. -
pentalty_dist_from_pam
(float, optional): penalty for offtarget wrt distance from PAM. Defaults to 0.1. -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
tuple
: tables
Note:
- Low value corresponds to high penalty and vice versa, because values are multiplied. 2. High penalty means consequential offtarget alignment and vice versa.
score_guides
function score_guides(
guides: DataFrame,
scores: DataFrame,
not_be: bool = False
) → DataFrame
Score guides
Args:
-
guides
(pd.DataFrame): guides -
scores
(pd.DataFrame): scores -
not_be
(bool, optional): not a base editor. Defaults to False.
Returns:
-
pd.DataFrame
: output table
Changes: penalty_activity_window disabled as only the sgRNAs with target in the window are reported.
beditor.lib.io
module Input/Output
download_annots
function download_annots(species_name: str, release: int) → bool
Download annotations using pyensembl
Args:
-
species_name
(str): species name -
release
(int): release number
Returns:
-
bool
: whether annotation is downloaded or not
cache_subdirectory
function cache_subdirectory(
reference_name: str = None,
annotation_name: str = None,
annotation_version: int = None,
CACHE_BASE_SUBDIR: str = 'beditor'
) → str
Which cache subdirectory to use for a given annotation database over a particular reference. All arguments can be omitted to just get the base subdirectory for all pyensembl cached datasets.
Args:
-
reference_name
(str, optional): reference name. Defaults to None. -
annotation_name
(str, optional): annotation name. Defaults to None. -
annotation_version
(int, optional): annotation version. Defaults to None. -
CACHE_BASE_SUBDIR
(str, optional): cache path. Defaults to 'beditor'.
Returns:
-
str
: output path
cached_path
function cached_path(path_or_url: str, cache_directory_path: str)
When downloading remote files, the default behavior is to name local files the same as their remote counterparts.
to_downloaded_cached_path
function to_downloaded_cached_path(
url: str,
annots=None,
reference_name: str = None,
annotation_name: str = 'ensembl',
ensembl_release: str = None,
CACHE_BASE_SUBDIR: str = 'pyensembl'
) → str
To downloaded cached path
Args:
-
url
(str): URL -
annots
(optional): pyensembl annotation. Defaults to None. -
reference_name
(str, optional): reference name. Defaults to None. -
annotation_name
(str, optional): annotation name. Defaults to 'ensembl'. -
ensembl_release
(str, optional): ensembl release. Defaults to None. -
CACHE_BASE_SUBDIR
(str, optional): cache path. Defaults to 'pyensembl'.
Returns:
-
str
: output path
download_genome
function download_genome(
species: str,
ensembl_release: int,
force: bool = False,
verbose: bool = False
) → str
Download genome
Args:
-
species
(str): species name -
ensembl_release
(int): release -
force
(bool, optional): force. Defaults to False. -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
str
: output path
read_genome
function read_genome(genome_path: str, fast=True)
Read genome
Args:
-
genome_path
(str): genome path -
fast
(bool, optional): fast mode. Defaults to True.
to_fasta
function to_fasta(
sequences: dict,
output_path: str,
molecule_type: str,
force: bool = True,
**kws_SeqRecord
) → str
Save fasta file.
Args:
-
sequences
(dict): dictionary mapping the sequence name to the sequence. -
output_path
(str): path of the fasta file. -
force
(bool): overwrite if file exists.
Returns:
-
output_path
(str): path of the fasta file
to_2bit
function to_2bit(
genome_path: str,
src_path: str = None,
force: bool = False,
verbose: bool = False
) → str
To 2bit
Args:
-
genome_path
(str): genome path -
src_path
(str, optional): source path. Defaults to None. -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
str
: output path
to_fasta_index
function to_fasta_index(
genome_path: str,
bgzip: bool = False,
bgzip_path: str = None,
threads: int = 1,
verbose: bool = True,
force: bool = False,
indexed: bool = False
) → str
To fasta index
Args:
-
genome_path
(str): genome path -
bgzip_path
(str, optional): bgzip path. Defaults to None. -
threads
(int, optional): threads. Defaults to 1. -
verbose
(bool, optional): verbose. Defaults to True. -
force
(bool, optional): force. Defaults to False. -
indexed
(bool, optional): indexed or not. Defaults to False.
Returns:
-
str
: output path
to_bed
function to_bed(
df: DataFrame,
outp: str,
cols: list = ['chrom', 'start', 'end', 'locus', 'score', 'strand']
) → str
To bed path
Args:
-
df
(pd.DataFrame): input table -
outp
(str): output path -
cols
(list, optional): columns. Defaults to ['chrom','start','end','locus','score','strand'].
Returns:
-
str
: output path
read_bed
function read_bed(
p: str,
cols: list = ['chrom', 'start', 'end', 'locus', 'score', 'strand']
) → DataFrame
Read bed file
Args:
-
p
(str): path -
cols
(list, optional): columns. Defaults to ['chrom','start','end','locus','score','strand'].
Returns:
-
pd.DataFrame
: output table
to_viz_inputs
function to_viz_inputs(
gtf_path: str,
genome_path: str,
output_dir_path: str,
output_ext: str = 'tsv',
threads: int = 1,
force: bool = False
) → dict
To viz inputs for the IGV
Args:
-
gtf_path
(str): GTF path -
genome_path
(str): genome path -
output_dir_path
(str): output directory path -
output_ext
(str, optional): output extension. Defaults to 'tsv'. -
threads
(int, optional): threads. Defaults to 1. -
force
(bool, optional): force. Defaults to False.
Returns:
-
dict
: configuration
to_igv_path_prefix
function to_igv_path_prefix() → str
Get IGV path prefix
Returns:
-
str
: URL
to_session_path
function to_session_path(p: str, path_prefix: str = None, outp: str = None) → str
To session path
Args:
-
p
(str): session configuration path -
path_prefix
(str, optional): path prefix. Defaults to None. -
outp
(str, optional): output path. Defaults to None.
Returns:
-
str
: output path
read_cytobands
function read_cytobands(
cytobands_path: str,
col_chrom: str = 'chromosome',
remove_prefix: str = 'chr'
) → DataFrame
Read cytobands
Args:
-
cytobands_path
(str): path -
col_chrom
(str, optional): column with contig. Defaults to 'chromosome'.
Returns:
-
pd.DataFrame
: output table
to_output
function to_output(inputs: DataFrame, guides: DataFrame, scores: DataFrame) → DataFrame
To output table
Args:
-
inputs
(pd.DataFrame): inputs -
guides
(pd.DataFrame): guides -
scores
(pd.DataFrame): scores
Returns:
-
pd.DataFrame
: output table
beditor.lib.make_guides
module Designing the sgRNAs
get_guide_pam
function get_guide_pam(
match: str,
pam_stream: str,
guidel: int,
seq: str,
pos_codon: int = None
)
get_pam_searches
function get_pam_searches(dpam: DataFrame, seq: str, pos_codon: int) → DataFrame
Search PAM occurance
:param dpam: dataframe with PAM sequences :param seq: target sequence :param pos_codon: reading frame :param test: debug mode on :returns dpam_searches: dataframe with positions of pams
get_guides
function get_guides(
data: DataFrame,
dpam: DataFrame,
guide_len: int,
base_fraction_max: float = 0.8
) → DataFrame
Get guides
Args:
-
data
(pd.DataFrame): input table -
dpam
(pd.DataFrame): table with PAM info -
guide_len
(int): guide length -
base_fraction_max
(float, optional): base fraction max. Defaults to 0.8.
Returns:
-
pd.DataFrame
: output table
to_locusby_pam
function to_locusby_pam(
chrom: str,
pam_start: int,
pam_end: int,
pam_position: str,
strand: str,
length: int,
start_off: int = 0
) → str
To locus by PAM from PAM coords.
Args:
-
chrom
(str): chrom -
pam_start
(int): PAM start -
pam_end
(int): PAM end -
pam_position
(str): PAM position -
strand
(str): strand -
length
(int): length
Returns:
-
str
: locus
to_pam_coord
function to_pam_coord(
startf: int,
endf: int,
startp: int,
endp: int,
strand: str
) → tuple
To PAM coordinates
Args:
-
startf
(int): start flank start -
endf
(int): start flank end -
startp
(int): start PAM start -
endp
(int): start PAM end -
strand
(str): strand
Returns:
-
tuple
: start,end
get_distances
function get_distances(df2: DataFrame, df3: DataFrame, cfg_method: dict) → DataFrame
Get distances
Args:
-
df2
(pd.DataFrame): input table #1 -
df3
(pd.DataFrame): input table #2 -
cfg_method
(dict): config for the method
Returns:
-
pd.DataFrame
: output table
get_windows_seq
function get_windows_seq(s: str, l: str, wl: str, verbose: bool = False) → str
Sequence by guide strand
Args:
-
s
(str): sequence -
l
(str): locus -
wl
(str): window locus -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
str
: window sequence
filter_guides
function filter_guides(
df1: DataFrame,
cfg_method: dict,
verbose: bool = False
) → DataFrame
Filter sgRNAs
Args:
-
df1
(pd.DataFrame): input table -
cfg_method
(dict): config of the method -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
pd.DataFrame
: output table
get_window_target_overlap
function get_window_target_overlap(
tstart: int,
tend: int,
wl: str,
ws: str,
nt: str,
verbose: bool = False
) → tuple
Get window target overlap
Args:
-
tstart
(int): target start -
tend
(int): target end -
wl
(str): window locus -
ws
(str): window sequence -
nt
(str): nucleotide -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
tuple
: window_overlaps_the_target,wts,nt_in_overlap,wtl
get_mutated_codon
function get_mutated_codon(
ts: str,
tl: str,
tes: str,
tel: str,
strand: str,
verbose: bool = False
) → str
Get mutated codon
Args:
-
ts
(str): target sequence -
tl
(str): target locus -
tes
(str): target edited sequence -
tel
(str): target edited locus -
strand
(str): strand -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
str
: mutated codon
get_coedits_base
function get_coedits_base(
ws: str,
wl: str,
wts: str,
wtl: str,
nt: str,
verbose: bool = False
) → str
Get co-edited bases
Args:
-
ws
(str): window sequence -
wl
(str): window locus -
wts
(str): window target overlap sequence -
wtl
(str): window target overlap locus -
nt
(str): nucleotide -
verbose
(bool, optional): verbose. Defaults to False.
Returns:
-
str
: coedits
beditor.lib
module
beditor.lib.methods
module Global Variables
- multint2reg
- multint2regcomplement
dpam2dpam_strands
function dpam2dpam_strands(dpam: DataFrame, pams: list) → DataFrame
Duplicates dpam dataframe to be compatible for searching PAMs on - strand
Args:
-
dpam
(pd.DataFrame): dataframe with pam information -
pams
(list): pams to be used for actual designing of guides.
Returns:
-
pd.DataFrame
: table
get_be2dpam
function get_be2dpam(
din: DataFrame,
methods: list = None,
test: bool = False,
cols_dpam: list = ['PAM', 'PAM position', 'guide length']
) → dict
Make BE to dpam mapping i.e. dict
Args:
-
din
(pd.DataFrame): table with BE and PAM info all cols_dpam needed -
methods
(list, optional): method names. Defaults to None. -
test
(bool, optional): test-mode. Defaults to False. -
cols_dpam
(list, optional): columns to be used. Defaults to ['PAM', 'PAM position', 'guide length'].
Returns:
-
dict
: output dictionary.
beditor.lib.utils
module Utilities
Global Variables
- cols_muts
- multint2reg
- multint2regcomplement
get_src_path
function get_src_path() → str
Get the beditor source directory path.
Returns:
-
str
: path
runbashcmd
function runbashcmd(cmd: str, test: bool = False, logf=None)
Run a bash command
Args:
-
cmd
(str): command -
test
(bool, optional): test-mode. Defaults to False. -
logf
(optional): log file instance. Defaults to None.
log_time_elapsed
function log_time_elapsed(start)
Log time elapsed.
Args:
-
start
(datetime): start tile
Returns:
-
datetime
: difference in time.
rescale
function rescale(
a: <built-in function array>,
mn: float = None
) → <built-in function array>
Rescale a vector.
Args:
-
a
(np.array): vector. -
mn
(float, optional): minimum value. Defaults to None.
Returns:
-
np.array
: output vector
get_nt2complement
function get_nt2complement()
s2re
function s2re(s: str, ss2re: dict) → str
String to regex patterns
Args:
-
s
(str): string -
ss2re
(dict): substrings to regex patterns.
Returns:
-
str
: string with regex patterns.
parse_locus
function parse_locus(s: str, zero_based: bool = True) → tuple
parse_locus summary
Args:
-
s
(str): location string. -
zero_based
(bool, optional): zero-based coordinates. Defaults to True.
Returns:
-
tuple
: chrom, start, end, strand
Notes:
beditor outputs (including bed files) use 0-based loci pyensembl and IGV use 1-based locations
get_pos
function get_pos(s: str, l: str, reverse: bool = True, zero_based: bool = True) → Series
Expand locus to positions mapped to nucleotides.
Args:
-
s
(str): sequence -
l
(str): locus -
reverse
(bool, optional): reverse the - strand. Defaults to True. -
zero_based
(bool, optional): zero based coordinates. Defaults to True.
Returns:
-
pd.Series
: output.
get_seq
function get_seq(
genome: str,
contig: str,
start: int,
end: int,
strand: str,
out_type: str = 'str',
verbose: bool = False
) → str
Extract a sequence from a genome file based on start and end positions using streaming.
Args:
-
genome
(str): The path to the genome file in FASTA format. -
contig
(str): chrom -
start
(int): start -
end
(int): end -
strand
(str): strand -
out_type
(str, optional): type of the output. Defaults to 'str'. -
verbose
(bool, optional): verbose. Defaults to False.
Raises:
-
ValueError
: invalid strand.
Returns:
-
str
: The extracted sequence.
read_fasta
function read_fasta(
fap: str,
key_type: str = 'id',
duplicates: bool = False,
out_type='dict'
) → dict
Read fasta
Args:
-
fap
(str): path -
key_type
(str, optional): key type. Defaults to 'id'. -
duplicates
(bool, optional): duplicates present. Defaults to False.
Returns:
-
dict
: data.
Notes:
- If
duplicates
key_type is set todescription
instead ofid
.
format_coords
function format_coords(df: DataFrame) → DataFrame
Format coordinates
Args:
-
df
(pd.DataFrame): table
Returns:
-
pd.DataFrame
: formated table
fetch_sequences_bp
function fetch_sequences_bp(p: str, genome: str) → DataFrame
Fetch sequences using biopython.
Args:
-
p
(str): path to the bed file. -
genome
(str): genome path.
Returns:
-
pd.DataFrame
: sequences.
fetch_sequences
function fetch_sequences(
p: str,
genome_path: str,
outp: str = None,
src_path: str = None,
revcom: bool = True,
method='2bit',
out_type='df'
) → DataFrame
Fetch sequences
Args:
-
p
(str): path to the bed file -
genome_path
(str): genome path -
outp
(str, optional): output path for fasta file. Defaults to None. -
src_path
(str, optional): source path. Defaults to None. -
revcom
(bool, optional): reverse-complement. Defaults to True. -
method
(str, optional): method name. Defaults to '2bit'. -
out_type
(str, optional): type of the output. Defaults to 'df'.
Returns:
-
pd.DataFrame
: sequences.
get_sequences
function get_sequences(
df1: DataFrame,
p: str,
genome_path: str,
outp: str = None,
src_path: str = None,
revcom: bool = True,
out_type: str = 'df',
renames: dict = {},
**kws_fetch_sequences
) → DataFrame
Get sequences for the loci in a table
Args:
-
df1
(pd.DataFrame): input table -
p
(str): path to the beb file -
outp
(str, optional): output path. Defaults to None. -
src_path
(str, optional): source path. Defaults to None. -
revcom
(bool, optional): reverse complement. Defaults to True. -
out_type
(str, optional): output type. Defaults to 'df'. -
renames
(dict, optional): renames. Defaults to {}.
Returns:
-
pd.DataFrame
: output sequences
Notes:
Input is 1-based Output is 0-based Saves bed file and gets the sequences
to_locus
function to_locus(
chrom: str = 'chrom',
start: str = 'start',
end: str = 'end',
strand: str = 'strand',
x: Series = None
) → str
To locus
Args:
-
chrom
(str, optional): chrom. Defaults to 'chrom'. -
start
(str, optional): strart. Defaults to 'start'. -
end
(str, optional): end. Defaults to 'end'. -
strand
(str, optional): strand. Defaults to 'strand'. -
x
(pd.Series, optional): row of the dataframe. Defaults to None.
Returns:
-
str
: locus
get_flanking_seqs
function get_flanking_seqs(
df1: DataFrame,
targets_path: str,
flanks_path: str,
genome: str = None,
search_window: list = None
) → DataFrame
Get flanking sequences
Args:
-
df1
(pd.DataFrame): input table -
targets_path
(str): target sequences path -
flanks_path
(str): flank sequences path -
genome
(str, optional): genome path. Defaults to None. -
search_window
(list, optional): search window around the target. Defaults to None.
Returns:
-
pd.DataFrame
: output table with sequences
get_strand
function get_strand(
genome,
df1: DataFrame,
col_start: str,
col_end: str,
col_chrom: str,
col_strand: str,
col_seq: str
) → DataFrame
Get strand by comparing the aligned and fetched sequence
Args:
-
genome
: genome instance -
df1
(pd.DataFrame): input table. -
col_start
(str): start -
col_end
(str): end -
col_chrom
(str): chrom -
col_strand
(str): strand -
col_seq
(str): sequences
Returns:
-
pd.DataFrame
: output table
Notes:
used for tests.
reverse_complement_multintseq
function reverse_complement_multintseq(seq: str, nt2complement: dict) → str
Reverse complement multi-nucleotide sequence
Args:
-
seq
(str): sequence -
nt2complement
(dict): nucleotide to complement
Returns:
-
str
: sequence
reverse_complement_multintseqreg
function reverse_complement_multintseqreg(
seq: str,
multint2regcomplement: dict,
nt2complement: dict
) → str
Reverse complement multi-nucleotide regex patterns
Args:
-
seq
(str): description -
multint2regcomplement
(dict): mapping. -
nt2complement
(dict): nucleotide to complement
Returns:
-
str
: regex pattern
hamming_distance
function hamming_distance(s1: str, s2: str) → int
Return the Hamming distance between equal-length sequences
Args:
-
s1
(str): sequence #1 -
s2
(str): sequence #2
Raises:
-
ValueError
: Undefined for sequences of unequal length
Returns:
-
int
: distance.
align
function align(
q: str,
s: str,
test: bool = False,
psm: float = 2,
pmm: float = 0.5,
pgo: float = -3,
pge: float = -1
) → str
Creates pairwise local alignment between seqeunces.
Args:
-
q
(str): query -
s
(str): subject -
test
(bool, optional): test-mode. Defaults to False.
Returns:
-
str
: alignment with symbols.
Notes:
REF: http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html The match parameters are: CODE DESCRIPTION x No parameters. Identical characters have score of 1, otherwise 0. m A match score is the score of identical chars, otherwise mismatch score. d A dictionary returns the score of any pair of characters. c A callback function returns scores. The gap penalty parameters are: CODE DESCRIPTION x No gap penalties. s Same open and extend gap penalties for both sequences. d The sequences have different open and extend gap penalties. c A callback function returns the gap penalties.
get_orep
function get_orep(seq: str) → int
Get the overrepresentation
get_polyt_length
function get_polyt_length(s: str) → int
Counts the length of the longest polyT stretch (RNA pol3 terminator) in sequence
:param s: sequence in string format
get_annots_installed
function get_annots_installed() → DataFrame
Get a list of annotations installed.
Returns:
-
pd.DataFrame
: output.
get_annots
function get_annots(
species_name: str = None,
release: int = None,
gtf_path: str = None,
transcript_path: str = None,
protein_path: str = None,
reference_name: str = 'assembly',
annotation_name: str = 'source',
verbose: bool = False,
**kws_Genome
)
Get pyensembl annotation instance
Args:
-
species_name
(str, optional): species name. Defaults to None. -
release
(int, optional): release number. Defaults to None. -
gtf_path
(str, optional): GTF path. Defaults to None. -
transcript_path
(str, optional): transcripts path. Defaults to None. -
protein_path
(str, optional): protein path. Defaults to None. -
reference_name
(str, optional): reference name. Defaults to 'assembly'. -
annotation_name
(str, optional): annotation name. Defaults to 'source'. -
verbose
(bool, optional): verbose. Defaults to False.
Returns: pyensembl annotation instance
to_pid
function to_pid(annots, gid: str) → str
To protein ID
Args:
-
annots
: pyensembl annotation instance -
gid
(str): gene ID
Returns:
-
str
: protein ID
to_one_based_coordinates
function to_one_based_coordinates(df: DataFrame) → DataFrame
To one based coordinates
Args:
-
df
(pd.DataFrame): input table
Returns:
-
pd.DataFrame
: output table.
beditor.lib.viz
module Visualizations.
to_igv
function to_igv(
cfg: dict = None,
gtf_path: str = None,
genome_path: str = None,
output_dir_path: str = None,
threads: int = 1,
output_ext: str = None,
force: bool = False
) → str
To IGV session file.
Args:
-
cfg
(dict, optional): configuration of the run. Defaults to None. -
gtf_path
(str, optional): path to the gtf file. Defaults to None. -
genome_path
(str, optional): path to the genome file. Defaults to None. -
output_dir_path
(str, optional): path to the output directory. Defaults to None. -
threads
(int, optional): threads. Defaults to 1. -
output_ext
(str, optional): extension of the output. Defaults to None. -
force
(bool, optional): force. Defaults to False.
Returns:
-
str
: path to the session file.
get_nt_composition
function get_nt_composition(seqs: list) → DataFrame
Get nt composition.
Args:
-
seqs
(list): list of sequences
Returns:
-
pd.DataFrame
: table with the frequencies of the nucleotides.
plot_ntcompos
function plot_ntcompos(
seqs: list,
pam_pos: str,
pam_len: int,
window: list = None,
ax: Axes = None,
color_pam: str = 'lime',
color_window: str = 'gold'
) → Axes
Plot nucleotide composition
Args:
-
seqs
(list): list of sequences. -
pam_pos
(str): PAM position. -
pam_len
(int): PAM length. -
window
(list, optional): activity window bounds. Defaults to None. -
ax
(plt.Axes, optional): subplot. Defaults to None. -
color_pam
(str, optional): color of the PAM. Defaults to 'lime'. -
color_window
(str, optional): color of the wnindow. Defaults to 'gold'.
Returns:
-
plt.Axes
: subplot
plot_ontarget
function plot_ontarget(
guide_loc: str,
pam_pos: str,
pam_len: int,
guidepam_seq: str,
window: list = None,
show_title: bool = False,
figsize: list = [10, 2],
verbose: bool = False,
kws_sg: dict = {}
) → Axes
plot_ontarget summary
Args:
-
guide_loc
(str): sgRNA locus -
pam_pos
(str): PAM position -
pam_len
(int): PAM length -
guidepam_seq
(str): sgRNA and PAM sequence -
window
(list, optional): activity window bounds. Defaults to None. -
show_title
(bool, optional): show the title. Defaults to False. -
figsize
(list, optional): figure size. Defaults to [10,2]. -
verbose
(bool, optional): verbose. Defaults to False. -
kws_sg
(dict, optional): keyword arguments to plot the sgRNA. Defaults to {}.
Returns:
-
plt.Axes
: subplot
TODOs: 1. convert to 1-based coordinates 2. features from the GTF file
get_plot_inputs
function get_plot_inputs(df2: DataFrame) → list
Get plot inputs.
Args:
-
df2
(pd.DataFrame): table.
Returns:
-
list
: list of tables.
plot_library_stats
function plot_library_stats(
dfs: list,
palette: dict = {True: 'b', False: 'lightgray'},
cutoffs: dict = None,
not_be: bool = True,
dbug: bool = False,
figsize: list = [10, 2.5]
) → list
Plot library stats
Args:
-
dfs
(list): list of tables. -
palette
(type, optional): color palette. Defaults to {True:'b',False:'lightgray'}. -
cutoffs
(dict, optional): cutoffs to be applied. Defaults to None. -
not_be
(bool, optional): not a base editor. Defaults to True. -
dbug
(bool, optional): debug mode. Defaults to False. -
figsize
(list, optional): figure size. Defaults to [10,2.5].
Returns:
-
list
: list of subplots.
beditor.run
module Command-line options
validate_params
function validate_params(parameters: dict) → bool
Validate the parameters.
Args:
-
parameters
(dict): parameters
Returns:
-
bool
: whther the parameters are valid or not
cli
function cli(
editor: str = None,
mutations_path: str = None,
output_dir_path: str = None,
species: str = None,
ensembl_release: int = None,
genome_path: str = None,
gtf_path: str = None,
rna_path: str = None,
prt_path: str = None,
search_window: int = None,
not_be: bool = False,
config_path: str = None,
wd_path: str = None,
threads: int = 1,
kernel_name: str = 'beditor',
verbose='WARNING',
igv_path_prefix=None,
ext: str = None,
force: bool = False,
dbug: bool = False,
skip=None,
**kws
)
beditor command-line (CLI)
Args:
-
editor
(str, optional): base-editing method, available methods can be listed using command: 'beditor resources'. Defaults to None. -
mutations_path
(str, optional): path to the mutation file, the format of which is available at https://github.com/rraadd88/beditor/README.md#Input-format. Defaults to None. -
output_dir_path
(str, optional): path to the directory where the outputs should be saved. Defaults to None. -
species
(str, optional): species name. Defaults to None. -
ensembl_release
(int, optional): ensemble release number. Defaults to None. -
genome_path
(str, optional): path to the genome file, which is not available on Ensembl. Defaults to None. -
gtf_path
(str, optional): path to the gene annotations file, which is not available on Ensembl. Defaults to None. -
rna_path
(str, optional): path to the transcript sequences file, which is not available on Ensembl. Defaults to None. -
prt_path
(str, optional): path to the protein sequences file, which is not available on Ensembl. Defaults to None. -
search_window
(int, optional): number of bases to search on either side of a target, if not specified, it is inferred by beditor. Defaults to None. -
not_be
(bool, optional): do not process as a base editor. Defaults to False. -
config_path
(str, optional): path to the configuration file. Defaults to None. -
wd_path
(str, optional): path to the working directory. Defaults to None. -
threads
(int, optional): number of threads. Defaults to 1. -
kernel_name
(str, optional): name of the jupyter kernel. Defaults to "beditor". -
verbose
(str, optional): verbose, logging levels: DEBUG > INFO > WARNING > ERROR (default) > CRITICAL. Defaults to "WARNING". -
igv_path_prefix
(type, optional): prefix to be added to the IGV url. Defaults to None. -
ext
(str, optional): file extensions of the output tables. Defaults to None. -
force
(bool, optional): overwrite the outputs of they exist. Defaults to False. -
dbug
(bool, optional): debug mode (developer). Defaults to False. -
skip
(type, optional): skip sections of the workflow (developer). Defaults to None.
Examples: beditor cli -c inputs/mutations/protein/positions.yml
Notes:
Required parameters for a run: editor mutations_path output_dir_path or config_path
gui
function gui()
resources
function resources()