cookbook.md

grepq cookbook

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 summarise command

grepq summarise -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 no more than 100000 matches, 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 no more than 100000 matches 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 no more than 100000 matches 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

As above, but uses the summarise command to ensure that all FASTQ records are processed

grepq --read-gzip regex.json file.fastq.gz summarise -c --names --json-matches

For each matched pattern in a search of no more than 100000 matches 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

As above, but uses the summarise command to ensure that all FASTQ records are processed

grepq --read-gzip regex.json file.fastq.gz summarise -c --names --json-matches --variants 3

For each matched pattern in a search of no more than 100000 matches 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

As above, but uses the summarise command to ensure that all FASTQ records are processed

grepq --read-gzip regex.json file.fastq.gz summarise -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

For a gzip-compressed FASTQ file, bucket matched sequences into separate files named after each regexName, with the output in FASTQ format

grepq -R --bucket --read-gzip regex.json file.fastq.gz

For a gzip-compressed FASTQ file, bucket matched sequences into separate files named after each regexName, with the output in FASTQ format, and write a SQLite database file, limiting the number of tetranucleotides in the TNF and CTNF fields to two

grepq -R --read-gzip --writeSQL -N 2 --bucket regex.json file.fastq.gz