diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 74db94f..a68a93e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: hooks: - id: isort-project name: isort_project - entry: isort -rc sensospot_data + entry: isort -rc sensospot_parser language: system pass_filenames: false - id: isort-test @@ -22,12 +22,12 @@ repos: pass_filenames: false - id: black name: black - entry: black sensospot_data tests + entry: black sensospot_parser tests language: system pass_filenames: false - id: flake8 name: flake8 - entry: flake8 --ignore E231,W503 sensospot_data tests + entry: flake8 --ignore E231,W503 sensospot_parser tests language: system pass_filenames: false - id: pytest diff --git a/README.md b/README.md index ba5622a..6f00ce3 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,21 @@ Sensospot Data Parser ===================== -Parsing the numerical output from Sensovation Sensospot image analysis. +Parsing the numerical output from [SensoSpot][sensospot] microarray analysis. + +The [SensoSpot][sensospot] microarray analyzer is an automated fluorescence microscope with an image analysis software for detecting and measuring microarrays. The original name of the product was "FLAIR" by the company Sensovation, that was later acquired by Miltenyi. + +There is no affiliation on my side regarding Sensovation or Miltenyi, I just use the product and needed a way to make the data available for further analysis. + ## Example: ```python - import sensospot_data + import sensospot_parser # read the raw data of a folder - raw_data = sensospot_data.parse_folder() + raw_data = sensospot_parser.parse_folder() sorted(raw_data.columns) == [ 'Analysis.Name', @@ -30,15 +35,14 @@ There is a `columns` module available, providing constans that define the column ```python - import sensospot_data + import sensospot_parser - sensospot_data.columns.ANALYSIS_NAME == "Analysis.Name" + sensospot_parser.columns.ANALYSIS_NAME == "Analysis.Name" ``` ## Avaliable public functions: -from sensospot_data import parse_file, parse_folder # noqa: F401 - **parse_folder(path_to_folder)** Searches the folder for parsable Sensospot .csv files, parses them into one big pandas data frame and will add additional meta data from parameters folder, @@ -76,3 +80,6 @@ To install the development version of Sensovation Data Parser: make devenv To run the tests, use `make tests` (failing on first error) or `make coverage` for a complete report. + + +[sensospot]: https://www.miltenyi-imaging.com/products/sensospot \ No newline at end of file