A Python library to simplify and support the execution of FragPipe when running in command-line mode.
It provides an interface to add a FASTA path to an existing workflow, handling the generation of manifest files from SDRF, and executing FragPipe.
The current version of fragpipe-runner has been tested with FragPipe version 23 on Windows 11, running an LFQ workflow with DDA data.
You can install the package from PyPI using pip:
pip install fragpipe-runnerHere is a simple example of how to use the library to run a FragPipe workflow with a specified manifest file:
import fragpipe_runner
fragpipe_runner.run_fragpipe(
fragpipe_dir="path/to/fragpipe_23-1",
workflow_path="path/to/workflow.workflow",
manifest_path="path/to/manifest.fp-manifest",
output_directory="path/to/output/directory",
)To create a manifest file from an SDRF file, you can use the following code (note that experiments using isobaric mass tags like TMT are not yet supported):
fragpipe_runner.manifest.sdrf_to_manifest(
sdrf_path="path/to/sdrf_file.tsv",
data_type="DDA",
manifest_filepath="output/path/of/manifest.fp-manifest",
experiment_field="factor value[condition]",
replicate_field="characteristics[biological replicate]",
)
fragpipe_runner.manifest.update_rawfile_paths_in_manifest(
manifest_filepath="output/path/of/manifest.fp-manifest",
rawfile_directory="directory/containing/rawfiles"
)