Find-and-Replace on ChRIS

A ChRIS ds plugin for find-and-replace operations on text files using regular expressions.

Usage

singularity exec docker://docker.io/fnndsc/pl-re-sub:latest resub \
    --expression ... --replacement ... \
    --inputPathFilter ... incoming/ outgoing/

Files inside incoming/ matching the glob given by --inputPathFilder are processed and written to outgoing/.

--expression

A string representing a regular expression with matching groups to search for. Uses Python re syntax.

--replacement

A string which may include matching groups which should be used to replace occurrences of what is matched by the value given to --expression.

--ifs

Multiple operations can be chained one after the other using the --ifs option. The value passed to --ifs (default ||) is a delimiter between multiple regexes.

For example, if you wanted to first replace all B with A and then do a second pass through the line replacing all :( with :):

singularity exec docker://docker.io/fnndsc/pl-re-sub:latest resub \
    --expression 'B :\(' --replacement 'A :\)' --ifs ' ' \
    --inputPathFilter 'report_card.txt' incoming/ outgoing/

Chained operation support can be disabled by passing --ifs ''.

Examples

For every *.csv files in the directory incoming/, change dates from MM/DD/YYYY format to YYYY.MM.DD format, and saving the results into a new directory outgoing/:

# set up date to be found in the incoming/ directory
mkdir incoming/ outgoing/
mv ./data.csv incoming/data.csv

# convert date formats in all files and write results into outgoing/
singularity exec docker://docker.io/fnndsc/pl-re-sub:latest resub \
    --expression '(\d\d)/(\d\d)/(\d\d\d\d)' \
    --replacement '\3.\1.\2' \
    --inputPathFilter '*.csv' incoming/ outgoing/

Performance

Processing is serial using a single-thread. When you have a large number of files, you can do parallel processing using external tools such as ChRIS, sbatch, or GNU parallel.

Examples: TODO

(Un)Planned Features

• eval support for dynamic replacement text generation