SPARC Curation Tools

The sparc-curation-tool is part of the software that is used in the collection of tools used for mapping data to scaffolds.

Note

This project is under active development.

Install

SPARC dataset tools can be installed from PyPi.org with the following command:

pip install sparc-curation-tool

Usage

Scaffold Annotations:

How to use (can also be found using scaffold-annotations -h):

usage: scaffold_annotations.py [-h] [-m MAX_SIZE] [-r] [-f] dataset_dir

Check scaffold annotations for a SPARC dataset.

positional arguments:

dataset_dir

root directory for dataset that need to be annotated.

optional arguments:

-h, –help	show this help message and exit
-m MAX_SIZE, –max-size MAX_SIZE	Set the max size for metadata file. Default is 2MiB
-r, –report	Report any errors that were found.
-f, –fix	Fix any errors that were found.

Plot Annotations:

How to use (can also be found using plot-annotation -h):

usage: plot-annotation.exe [-h] [-x X_AXIS_COLUMN] [-y [Y_AXES_COLUMNS ...]] [-n] [-r] [-d {tab,comma}] {heatmap,timeseries}

Create an annotation for a SPARC plot. The Y_AXES_COLUMNS can either be single numbers or a range in the form 5-8. The start and end numbers are included in the range. The -y/–y-axes-columns argument will consume the positional plot type argument. That means the positional argument cannot follow the -y/–y-axes-columns.

positional arguments:

{heatmap,timeseries} must define a plot type which is one of; heatmap, timeseries.

positional arguments:

dataset_dir

root directory for dataset that need to be annotated.

optional arguments:

{heatmap,timeseries}	must define a plot type which is one of; heatmap, timeseries.
-h, –help	show this help message and exit
-x X_AXIS_COLUMN, –x-axis-column X_AXIS_COLUMN	integer index for the independent column (zero based). Default is 0.
-y [Y_AXES_COLUMNS …], –y-axes-columns [Y_AXES_COLUMNS …]	list of indices for the dependent columns (zero based). Can be used multiple times. Can be specified as a range e.g. 5-8. Default is [].
-n, –no-header	Boolean to indicate whether a header line is missing. Default is False.
-r, –row-major	Boolean to indicate whether the data is row major or column major. Default is False.
-d {tab,comma}, –delimiter {tab,comma}	The type of delimiter used, must be one of; tab, comma. Default is comma.

Run

To run the application create a virtual environment.

python -m venv venv_sparc

Activate the virtual environment:

source venv_sparc/bin/activate

For bash shells, or:

venv_sparc\Scripts\activate

For a windows cmd prompt.

With the activated virtual environment install the package.

pip install sparc-curation-tools

Then execute the application to print out the usage information to test the script.

Scaffold Annotations

scaffold-annotations -h

Plot Annotations

plot-annotations -h

Examples:

Scaffold Annotations

scaffold-annotations <dataset_dir>

Plot Annotations

plot-annotations <dataset_dir>