Summarise snps relative to a reference sequence
pip install snipit
Link to test data: test.fasta
- Basic usage for nucleotide alignments:
snipit test.fasta \
--output-file test
Default format output is png. Only specify output path/name (not extension).
- To change output format, use
--format:
snipit test.fasta \
--output-file test \
--format pdf
Options: png, jpg, pdf, svg, tiff.
- To change color scheme, use
--colour-palette:
snipit test.fasta \
--output-file test \
--colour-palette classic_extended
Other colours schemes:
classic, classic_extended, primary, purine-pyrimidine, greyscale, wes,verity, ugene
Use ugene for protein (aa) alignments.
Use classic_extended for colouring ambiguous bases.
- There are multiple options to control which SNPs or indels are included/excluded:
snipit test.fasta \
--show-indels \
--include-positions '100-150' \
--exclude-positions '223 224 225'
- For control over ambiguous bases, use
--ambig-modeto specify how ambiguous bases are handled:
[all] include all ambig such as N,Y,B in all positions
[snps] only include ambig if a snp is present at the same position - Default
[exclude] remove all ambig, same as depreciated --exclude-ambig-pos
Use the colour palette classic_extended when plotting with all or snps.
- Recombination mode is designed to assist with recombination analysis for SC2. This mode allows for colouring of mutations present in two references. For recombination mode, three flags are required:
--reference,--recombi-mode,--recombi-references.
The specified --reference must be different from the --recombi-references.
snipit test.fasta \
--reference USA_3 \
--recombi-mode \
--recombi-references "USA_1,USA_2"
For amino acid alignments, specify the sequence type as aa, use the colour palette ugene:
snipit test.prot.fasta \
--sequence-type aa \
--colour-palette ugene \
--output-file test.prot
There are several more options, see below for full usage.
snipit
optional arguments:
-h, --help show this help message and exit
Input options:
alignment Input alignment fasta file
-t {nt,aa}, --sequence-type {nt,aa}
Input sequence type: aa or nt
-r REFERENCE, --reference REFERENCE
Indicates which sequence in the alignment is the
reference (by sequence ID). Default: first sequence in
alignment
-l LABELS, --labels LABELS
Optional csv file of labels to show in output snipit
plot. Default: sequence names
--l-header LABEL_HEADERS
Comma separated string of column headers in label csv.
First field indicates sequence name column, second the
label column. Default: 'name,label'
Mode options:
--recombi-mode Allow colouring of query seqeunces by mutations
present in two 'recombi-references' from the input
alignment fasta file
--recombi-references RECOMBI_REFERENCES
Specify two comma separated sequence IDs in the input
alignment to use as 'recombi-references'. Ex.
Sequence_ID_A,Sequence_ID_B
--cds-mode Assumes sequence supplied is a coding sequence
Output options:
-d OUTPUT_DIR, --output-dir OUTPUT_DIR
Output directory. Default: current working directory
-o OUTFILE, --output-file OUTFILE
Output file name stem. Default: snp_plot
-s, --write-snps Write out the SNPs in a csv file.
-f FORMAT, --format FORMAT
Format options (png, jpg, pdf, svg, tiff) Default: png
Figure options:
--height HEIGHT Overwrite the default figure height
--width WIDTH Overwrite the default figure width
--size-option SIZE_OPTION
Specify options for sizing. Options: expand, scale
--solid-background Force the plot to have a solid background, rather than
a transparent one.
-c , --colour-palette
Specify colour palette. Options: [classic,
classic_extended, primary, purine-pyrimidine,
greyscale, wes, verity, ugene]. Use ugene for protein
alignments.
--flip-vertical Flip the orientation of the plot so sequences are
below the reference rather than above it.
--sort-by-mutation-number
Render the graph with sequences sorted by the number
of SNPs relative to the reference (fewest to most).
Default: False
--sort-by-id Sort sequences alphabetically by sequence id. Default:
False
--sort-by-mutations SORT_BY_MUTATIONS
Sort sequences by bases at specified positions.
Positions are comma separated integers. Ex. '1,2,3'
--high-to-low If sorted by mutation number is selected, show the
sequences with the fewest SNPs closest to the
reference. Default: False
SNP options:
--show-indels Include insertion and deletion mutations in snipit
plot.
--include-positions INCLUDED_POSITIONS [INCLUDED_POSITIONS ...]
One or more range (closed, inclusive; one-indexed) or
specific position only included in the output. Ex.
'100-150' or Ex. '100 101' Considered before '--
exclude-positions'.
--exclude-positions EXCLUDED_POSITIONS [EXCLUDED_POSITIONS ...]
One or more range (closed, inclusive; one-indexed) or
specific position to exclude in the output. Ex.
'100-150' or Ex. '100 101' Considered after '--
include-positions'.
--ambig-mode {all,snps,exclude}
Controls how ambiguous bases are handled - [all]
include all ambig such as N,Y,B in all positions;
[snps] only include ambig if a snp is present at the
same position; [exclude] remove all ambig, same as
depreciated --exclude-ambig-pos
Misc options:
-v, --version show program's version number and exit
Please cite this tool as follows:
Aine O'Toole, snipit (2024) GitHub repository, https://github.com/aineniamh/snipit
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