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Metasplit

A program to split (very) large .csv files column-wise based on some other metadata file with minimal memory overhead.

Installation

This needs the xsv binary in your PATH, since it uses it as a backend to do the heavy lifting. Install it from the BurntSushi/xsv repository.

You need to have python 3.10 or later installed. Install metasplit with:

pip install git+https://github.com/MrHedmad/metasplit@main

Then you can use metasplit with the metasplit command.

Usage

Use metasplit --help for a list of arguments. The argument should be self-explaining with the exception of the selection strings. I explain them here.

A selection string is a structured strings with this form:

|--------------------| |---------||------------ >>>
/path/to/metadata/file@id_variable?meta_var1=value&meta_var2=value ...
                      ^           ^               ^

The query has many parts:

  • /path/to/metadata/file: The (full) path to the metadata file to use to select the columns of the input file with.
  • id_variable: The name of the column in the metadata file that holds the ids of the columns in the input file. Must be preceded by an @.
  • After these two parts, the rest of the string is made up by selections:
    • The first selection always starts with an ?. This marks the beginning of the selection strings.
    • Every selection is of the form variable + sign + value(s). The variable is the column to consider in the metadata. The value(s) are either one (value) or a list of ([value1,value2,value3]) of values to select the ids with. The sign might be either = or != for the variable being equal to or not equal to the values, respectively.
    • Multiple selections may be chained together by starting new selection strings with either & or | for a logical AND or a logical OR with the previous selection.

You can pass multiple selection strings as input, even from different metadata files. Each selection from every metadata file will be summed together (a sort of "OR") to subset the final data file. If you instead wish to only keep IDs that satisfy your selections in every metadata file (a sort of "AND"), you can pass the --intersect flag to do just that.

Examples

Some examples of query strings:

  • ~/metadata.csv@gene_id?sample_type=tumor: Read the ~/metadata.csv file, and select column ids in the gene_id column where the column sample_type is equal to tumor.
  • ~/metadata.csv@gene_id?type=[primary_tumor,metastasis]&study=tcga: Similar to the previous example, select where type is either primary_tumor or metastasis AND the study is tcga.
  • ~/metadata.csv@gene_id?study=tcga|selection=manually_selected: select where study is equal to tcga OR the selection is manually_selected.
  • ~/metadata.csv@sample_id?study=tcga ~/clinical_metadata.csv@patient_id?smoker=true|exposed_to_asbestos=true --intersect: select in the metadata.csv file where study is equal to tcga. Then, select in the clinical_metadata.csv file where smoker is true OR exposed_to_asbestos is true. Keep only samples that satisfy both selections (due to the --intersect flag).