snipit

Summarise snps relative to a reference sequence

Install

pip install snipit

Example Usage

Link to test data: test.fasta and aa_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-mode to 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.

Issues

If you see an error like: ModuleNotFoundError: No module named 'pkg_resources' This may mean your python install did not come with setuptools. Install setuptools and this should resolve the issue.

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 RECOMBIREFERENCES Specify two comma separated sequence IDs in the input alignment to use as 'recombi-references'. Ex. SequenceIDA,SequenceID_B --cds-mode Assumes sequence supplied is a coding sequence

Output options: -d OUTPUTDIR, --output-dir OUTPUTDIR 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 SIZEOPTION 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, classicextended, 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 SORTBYMUTATIONS 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 INCLUDEDPOSITIONS [INCLUDEDPOSITIONS ...] 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 EXCLUDEDPOSITIONS [EXCLUDEDPOSITIONS ...] 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 ```

Cite

Please cite this tool as follows: Aine O'Toole, snipit (2024) GitHub repository, https://github.com/aineniamh/snipit