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Snakemake utils

Project description

A set of utility function for use in snakemake. Currently, for line-based transformations.

Functions:

  • map_chars(cmap) - will translate characters using the given dictionary cmap.
  • del_char_idx(idx) - will delete the char at the given index.
  • del_char(char) - will delete all characters matching char param.
  • del_line(regex) - will delete line if it matches the given regex.
  • apply(trans, encoding, in_files, out_files) - will apply all transformations given in trans list to all lines in the in_files list producing output files from the out_files list.

Example

rule fixchars:
    input:
        "{natfile}.nat"
    output:
        "{natfile}-ch.nat"
    message:
        "Fixing/deleting chars/lines..."

    run:
        from snakemakeutils import del_char_val, del_char_idx, apply
        trans = [del_char_val('\x00'), del_char_idx(0)]
        apply(trans, "latin1", input, output)

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Files for snakemakeutils, version 0.1.2
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