https://github.com/aineniamh/snipit

snipit: summarise snps relative to your reference sequence
https://github.com/aineniamh/snipit

Last synced: 4 months ago
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snipit: summarise snps relative to your reference sequence

• Host: GitHub
• URL: https://github.com/aineniamh/snipit
• Owner: aineniamh
• License: gpl-3.0
• Created: 2020-09-15T11:23:05.000Z (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2024-02-16T01:40:52.000Z (5 months ago)
• Last Synced: 2024-03-17T13:03:41.713Z (4 months ago)
• Language: Python
• Size: 354 KB
• Stars: 104
• Watchers: 4
• Forks: 22
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - snpit - genome-visualization/snpit.png) (Variation)
• awesome-genome-visualization - snpit

README

        
# snipit

Summarise snps relative to a reference sequence



### Usage

```

usage: snipit  [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

```

### Install

```

pip install snipit

```