syntactic¶

Make syntactically valid names out of strings.

The package improves upon Python’s own name-sanitization idioms by adding smart handling of mixed-case acronyms (e.g. mRNA, RNAi), decimals, and other conventions commonly used in the life sciences.

The package works in two modes: string mode (default) and file rename mode. There are five primary naming functions:

camel_case (e.g. "helloWorld").
dotted_case (e.g. "hello.world").
snake_case (e.g. "hello_world").
kebab_case (e.g. "hello-world").
upper_camel_case (e.g. "HelloWorld").

Installation¶

uv method¶

This package is hosted at python.acidgenomics.com. We recommend using uv to install.

uv pip install \
    --index-url 'https://python.acidgenomics.com/simple/' \
    syntactic

Or add the index to your project’s pyproject.toml:

[[tool.uv.index]]
url = "https://python.acidgenomics.com/simple/"

Then install:

uv add syntactic

Conda method¶

Configure Conda to use the Bioconda channels.

# Don't install recipe into base environment.
name='syntactic'
conda create --name="$name" "$name"
conda activate "$name"
python -c 'import syntactic'

String mode¶

In general, stick with snake_case or camel_case when sanitizing character strings.

>>> from syntactic import camel_case, make_names, snake_case
>>> object = ["human genomeVersion", "sampleID"]

Use snake case formatting inside of scripts:

>>> snake_case(object)
['human_genome_version', 'sample_id']

Camel case is recommended inside of packages, for function and variable names. The package offers two variants: relaxed (default) or strict mode. Relaxed mode generally returns acronyms (e.g. ID) more legibly.

>>> camel_case(object, strict=False)
['humanGenomeVersion', 'sampleID']
>>> camel_case(object, strict=True)
['humanGenomeVersion', 'sampleId']

make_names sanitizes arbitrary strings into valid Python identifiers, underscore-separated:

>>> make_names(["%GC", "1st sample", "hello world"])
['GC', 'X1st_sample', 'hello_world']

Human-readable conversions¶

make_words and make_title go the other direction, converting a syntactic variable name back into readable prose:

>>> from syntactic import make_title, make_words
>>> make_words(["nGene", "log10GenesPerUMI"])
['n gene', 'log10 genes per UMI']
>>> make_title(["nGene", "log10GenesPerUMI"])
['N gene', 'Log10 genes per UMI']

File rename mode¶

The package also supports file name sanitization via syntactic_rename. This currently includes support for kebab_case (recommended), snake_case, and camel_case, via the fun argument:

>>> from syntactic import syntactic_rename
>>> syntactic_rename("/path/to/dir", fun="kebab_case")

Recursion into subdirectories is supported using recursive=True, and dry_run=True previews the renames without touching the filesystem.