IsoSLAM

IsoSLAM is a Python package for processing and working with SLAMSeq data of RNA expression.

Installation

IsoSLAM is available on the Python Package Index (PyPI). It is recommended to use a Python Virtual Environment and install within that.

pip install isoslam

You can also install IsoSLAM directly from this GitHub repository using pip...

pip install git+https://github.com/sudlab/IsoSLAM.git

Alternatively you can clone the repository and install it from there, optionally using the -e flag to make the code editable should you wish to work on developing the code base.

cd ~/path/to/clone/to
git clone git@github.com:sudlab/IsoSLAM.git
cd IsoSLAM
pip install -e .

If you wish to include optional dependencies you may do so.

pip install -e .[dev,docs,tests]

Conda/BioConda

If you use Conda or BioConda to manage your virtual environments and wish to document the installation of IsoSLAM in a YAML file you can add it as a pip dependency as shown in the sample isoslam.yaml file below which includes cgatcore and ruffus as dependencies which will be installed from one of the listed Conda channels.

name: isoslam

channels:
  - conda-forge
  - bioconda
  - default

dependencies:
  - cgatcore
  - ruffus
  - pip
  - pip:
      - isoslam

You can then create an environment using the following.

conda env create --name isoslam --file isoslam.yaml

Usage

On installation the isoslam entry point will be added to the $PATH of your Virtual Environment. You can then invoke it with the --help flag to see the available options.

❱ isoslam --help
usage: isoslam [-h] [-v] [-c CONFIG_FILE] [-b BASE_DIR] [-o OUTPUT_DIR] [-l LOG_LEVEL] {process,create-config,summary-counts} ...

Run various programs related to IsoSLAM. Add the name of the program you wish to run.

options:
  -h, --help            show this help message and exit
  -v, --version         Report the installed version of IsoSLAM.
  -c, --config-file CONFIG_FILE
                        Path to a YAML configuration file.
  -b, --base-dir BASE_DIR
                        Base directory to run isoslam on.
  -o, --output-dir OUTPUT_DIR
                        Output directory to write results to.
  -l, --log-level LOG_LEVEL
                        Logging level to use, default is 'info' for verbose output use 'debug'.

program:
  Available programs listed below:

  {process,create-config,summary-counts}
    process             Process all files and run all summary plotting and statistics.
    create-config       Create a configuration file using the defaults.
    summary-counts      Summarise the counts.

Each sub-command includes help too, for example...

❱ isoslam process --help
usage: isoslam process [-h] [-b BAM_FILE] [-g GTF_FILE] [-d BED_FILE] [-v VCF_FILE] [-u UPPER_PAIRS_LIMIT] [-f FIRST_MATCHED_LIMIT] [--delim DELIM]
                       [--output-file OUTPUT_FILE]

Process all files and run all summary plotting and statistics.

options:
  -h, --help            show this help message and exit
  -b, --bam-file BAM_FILE
                        Path to '.bam' file that has undergone read assignment with 'featureCount'.
  -g, --gtf-file GTF_FILE
                        Path to '.gtf' transcript assembly file.
  -d, --bed-file BED_FILE
                        Path to '.bed' utron file. Must be bed6 format.
  -v, --vcf-file VCF_FILE
                        Path to '.vcf.gz' file.
  -u, --upper-pairs-limit UPPER_PAIRS_LIMIT
                        Upper limit of pairs to be processed.
  -f, --first-matched-limit FIRST_MATCHED_LIMIT
                        Limit of matches.
  --delim DELIM         Delimiter to use in output.
  --output-file OUTPUT_FILE
                        File to write results to.

Including in Pipelines

Calls to this entry point can easily be incorporated into CGAT/ruffus or other pipelines.

How it Works

Contributing

Contributions are welcome. We have a Code of Conduct that we ask you respect.

If you have bugs or feature requests please create an issue, there are templates for reporting bugs and making feature requests.

If you wish to contribute fixes or features yourself you can find detailed information in the contributing document (which is rendered on the website).

Licence

This software is licensed as specified by the MIT License.

Citation

Please use the Citation File Format which is available in this repository. A BibTex or APA formatted citation can be easily accessed from the "Cite this repository" link on the right hand side.