genewiz-template-validator 0.0.11

G001 data entry validation for Genewiz templates.

Validate GENEWIZ template files, sample map templates and container templates.

Installation

1. Install pip

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py

2. Install the package

pip install -i https://test.pypi.org/simple/ genewiz-template-validator

3. Check if it works.

validate_genewiz_templates -h

To get help:

validate_genewiz_templates -h

usage: validate_genewiz_templates [-h]
                              container_template_name.xlsx
                              sample_template_name.xlsx
                              [sample_template_name.xlsx ...]
The following arguments are required:
    container_template_name.xlsx, sample_template_name.xlsx

To run this validator:

validate_genewiz_templates container_template.xlsx sample_template_1.xlsx sample_template_2.xlsx

The validator checks the following:

1. That the provided sample map and container template can be found and are readable.

2. That the sample map template files are listed in the container template.

3. That there are no extraneous sample map entries in the container template.

4. That the format of the sample id matches the expected naming scheme: G0015[89]xxx_Vxx_Pxx_R2_[HKL]C_[A-H]xx

In the event that any of these validation checks fail, the validator will exit with an error message and produce a “log” file GENEWIZ_template_validation.log in the current directory, that can be inspected to identify the errors it found and to correct them.