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
-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
--flip-vertical Flip the orientation of the plot so sequences are below the reference rather than above it.
--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 .
54F5
..]
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
--high-to-low If sorted by mutation number is selected, show the sequences with the fewest SNPs closest to the reference. Default: False
-c COLOUR_PALETTE, --colour-palette COLOUR_PALETTE
Specify colour palette. Options: primary, classic, purine-pyrimidine, greyscale, wes, verity
pip install snipit