Print the help message (including tips and notes)
grepq -h
and
grepq --help
Print the help message for the tune command
grepq tune -h
Print the help message for the inverted command
grepq inverted -h
Print only the matching sequences
grepq regex.txt file.fastq
Print the matching sequences with the record ID
grepq -I regex.txt file.fastq
Print the matching sequences in FASTQ format
grepq -R regex.txt file.fastq
Save the matching sequences in gzip compressed FASTQ format
grepq -R --write-gzip regex.txt file.fastq > output.fastq.gz
Read the FASTQ file in gzip compressed format
grepq --read-gzip regex.txt file.fastq.gz
Read and save the output in gzip compressed format, with fast compression
grepq --read-gzip --write-gzip --fast regex.txt file.fastq.gz > output.fastq.gz
Read and save the output in gzip compressed format, with best compression
grepq --read-gzip --write-gzip --best regex.txt file.fastq.gz > output.fastq.gz
Read and save the output in zstd compressed format, with best compression
grepq --read-zstd --write-zstd --best regex.txt file.fastq.zst > output.fastq.zst
Read and save the output in zstd compressed format, with fast compression
grepq --read-zstd --write-zstd --fast regex.txt file.fastq.zst > output.fastq.zst
Count the number of matching FASTQ records
grepq -c regex.txt file.fastq
For each matched pattern in a search of the first 100000 records, print the pattern and the number of matches
grepq regex.txt file.fastq tune -n 100000 -c
For each matched pattern in a search of the first 100000 records of a gzip-compressed FASTQ file, print the pattern and the number of matches
grepq --read-gzip regex.txt file.fastq.gz tune -n 100000 -c
For each matched pattern in a search of the first 100000 records of a gzip-compressed FASTQ file, print the pattern and the number of matches to a JSON file called matches.json
grepq --read-gzip regex.json file.fastq.gz tune -n 100000 -c --names --json-matches
For each matched pattern in a search of the first 100000 records of a gzip-compressed FASTQ file, print the pattern and the number of matches to a JSON file called matches.json, and include the top three most frequent variants of each pattern, and their respective counts
grepq --read-gzip regex.json file.fastq.gz tune -n 100000 -c --names --json-matches --variants 3
For each matched pattern in a search of the first 100000 records of a
gzip-compressed FASTQ file, print the pattern and the number of matches to a JSON
file called matches.json, and include all variants of each pattern, and their
respective counts. Note that the --variants argument is not given when --all
is specified."
grepq --read-gzip regex.json file.fastq.gz tune -n 100000 -c --names --json-matches --all
Print the records where none of the regex patterns are found
grepq regex.txt file.fastq inverted
Print the records where none of the regex patterns are found, with the record ID
grepq -I regex.txt file.fastq inverted
Print the records where none of the regex patterns are found, in FASTQ format
grepq -R regex.txt file.fastq inverted
Count the number of records where none of the regex patterns are found
grepq -c regex.txt file.fastq inverted
Count the total number of records in the FASTQ file using an empty pattern file
grepq -c empty.txt file.fastq inverted