github.com/Rbfinch/grepq @grepq-v1.08

quickly filter fastq files by matching sequences to a set of regex patterns

Performance

grepq is fast

On a Mac Studio with 32GB RAM and Apple M1 max chip, grepq processed a 104GB fastq file against 30 regex patterns in 88 seconds, about 1.2GB of fastq data per second. For a 874MB fastq file, it was around 4.8 and 450 times faster than the general-purpose regex tools ripgrep and grep, respectively, on the same hardware.

grepq does not match false positives

grepq will only match regex patterns to the sequence part of the fastq file, which is the most common use case. Unlike ripgrep and grep, which will match the regex patterns to the entire fastq record, which includes the record ID, sequence, separator, and quality. This can lead to false positives and slow down the filtering process.

Usage

Ouput from -h option

Usage: grepq [OPTIONS] <PATTERNS> <FILE>

Arguments:
  <PATTERNS>  Path to the patterns file (one regex pattern per line)
  <FILE>      Path to the fastq file

Options:
  -I             Include record ID in the output
  -R             Include record ID, sequence, separator, and quality in the output
  -c             Count the number of matching fastq records
  -h, --help     Print help (see more with '--help')
  -V, --version  Print version


       Examples:
             - Print only the matching sequences:
                  grepq regex.txt file.fastq > outfile.txt

             - Print the matching sequences with the record ID:
                  grepq -I regex.txt file.fastq > outfile.txt

             - Print the matching sequences with the record ID, sequence, separator, and quality fields
                  grepq -R regex.txt file.fastq > outfile.txt

             - Count the number of matching fastq records:
                  grepq -c regex.txt file.fastq

           Tips:
             - Order your regex patterns from those that are most likely to match to those that
               are least likely to match. This will speed up the filtering process.

             - Ensure you have enough storage space for the output file.

          Notes:
             - Only supports fastq files.

             - Patterns file must contain one regex pattern per line.

             - When no options are provided, only the matching sequences are printed.

             - Only one of the -I, -R, or -c options can be used at a time.

             - Count option (-c) will support the output of the -R option since it is in fastq format.

             - Inverted matches are not supported.

             - Regex patterns with look-around and backreferences are not supported.

Requirements

• grepq has been tested on Linux and macOS. It might work on Windows, but it has not been tested.
• Ensure that Rust is installed on your system (https://www.rust-lang.org/tools/install)

Installation

• From source

  • Clone the repository and cd into the grepq directory
  • Run cargo build --release
  • Relative to the cloned parent directory, the executable will be located in ./target/release
  • Make sure the executable is in your PATH or use the full path to the executable

• From crates.io (easiest method)

  • cargo install grepq

Checksums to verify grepq is working correctly, using the regex file regex.txt and the small fastq file small.fastq, both located in the test directory:

./target/release/grepq ./test/regex.txt ./test/small.fastq > outfile.txt
sha256sum outfile.txt # checksum of outfile.txt if no option is given
ed0527a4d03481a50b365b03f5d952afab1df259966021699484cd9d59d790fc

./target/release/grepq -I ./test/regex.txt ./test/small.fastq > outfile.txt
sha256sum outfile.txt # checksum of outfile.txt if -I option is given
204bec425495f606611ba20605c6fa6e6d10627fc3203126821a2df8af025fb0

./target/release/grepq -R ./test/regex.txt ./test/small.fastq > outfile.txt
sha256sum outfile.txt # checksum of outfile.txt if -R option is given
67ad581448b5e9f0feae96b11f7a48f101cd5da8011b8b27a706681f703c6caf

Update changes

see CHANGELOG

License

MIT