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 thein_files
list producing output files from theout_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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