Seaflowpy
A Python package for SeaFlow flow cytometer data.
Table of Contents
Install
This package is compatible with Python 3.10 and 3.11
Source
To install this project from a clone of the repo use poetry
poetry self add poetry-plugin-export
poetry self add "poetry-dynamic-versioning[plugin]"
poetry install
PyPI
pip install seaflowpy
Docker
Docker images are available from Docker Hub at ctberthiaume/seaflowpy.
docker pull ctberthiaume/seaflowpy
docker run -it ctberthiaume/seaflowpy seaflowpy version
The Docker build file is in this repo at /Dockerfile. The build process for the Docker image is detailed in /build-docker.sh.
Command-line interface
All seaflowpy CLI tools are accessible from the seaflowpy executable.
Run seaflowpy --help to begin exploring the CLI usage documentation.
SFL validation workflow
SFL validation sub-commands are available under the seaflowpy sfl command.
The usage details for each command can be accessed as seaflowpy sfl <cmd> -h.
The basic worfkflow should be
-
If starting with an SDS file, first convert to SFL with
seaflowpy sds2sfl -
If the SFL file is output from
sds2sflor is a raw SeaFlow SFL file, convert it to a normalized format withseaflowpy sfl print. This command can be used to concatenate multiple SFL files, e.g. merge all SFL files in day-of-year directories. -
Check for potential errors or warnings with
seaflowpy sfl validate. -
Fix errors and warnings. Duplicate file errors can be fixed with
seaflowpy sfl dedup. Bad lat/lon errors may be fixed withseaflowpy sfl convert-gga, assuming the bad coordinates are GGA to begin with. This can be checked with withseaflowpy sfl detect-gga. Other errors or missing values may need to be fixed manually. -
(Optional) Update event rates based on true event counts and file duration with
seaflowpy sfl fix-event-rate. True event counts for raw EVT files can be determined withseaflowpy evt count. If filtering has already been performed then event counts can be pulled from theall_countcolumn of the opp table in the SQLITE3 database. e.g.sqlite3 -separator $'\t' SCOPE_14.db 'SELECT file, all_count ORDER BY file' -
(Optional) As a check for dataset completeness, the list of files in an SFL file can be compared to the actual EVT files present with
seaflowpy sfl manifest. It's normal for a few files to differ, especially near midnight. If a large number of files are missing it may be a sign that the data transfer was incomplete or the SFL file is missing some days. -
Once all errors or warnings have been fixed, do a final
seaflowpy validatebefore adding the SFL file to the appropriate repository.
Configuration
To use seaflowpy sfl manifest AWS credentials need to be configured.
The easiest way to do this is to install the awscli Python package
and go through configuration.
pip3 install awscli
aws configure
This will store AWS configuration in ~/.aws which seaflowpy will use to
access Seaflow data in S3 storage.
Testing
Seaflowpy uses pytest for testing. Tests can be run from this directory as
pytest to test the installed version of the package.
1 maintainer
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