Summarise snps relative to a reference sequence
usage: snipit <alignment> [options]
snipit
positional arguments:
alignment Input alignment fasta file
optional arguments:
-h, --help show this help message and exit
-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'
-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
--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.
--flip-vertical Flip the orientation of the plot so sequences are below the
reference rather than above it.
--snps-only Ignore insertion and deletion mutations and only plot SNPs
(legacy behaviour).
--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'.
--exclude-ambig-pos Exclude positions with ambig base in any sequences. Considered
after '--include-positions'
--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
-v, --version show program's version number and exit
-c COLOUR_PALETTE, --colour-palette COLOUR_PALETTE
Specify colour palette. Options: primary, classic, purine-pyrimidine, greyscale, wes, verity
--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
pip install snipit