fqgrep

Grep for FASTQ files.

Search a pair of fastq files for reads that match a given ref or alt sequence.

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Install

From bioconda

conda install -c bioconda fqgrep

From Source

git clone ... && cd fqgrep
cargo install --path .

Usage

To match a single pattern in a single FASTQ:

fqgrep 'GACGAGATTA' /data/test.fastq.gz

To match two patterns across two FASTQs treating them as paired end:

fqgrep  --paired --threads 10 --regexp 'GACGAGATTA' --regexp 'GACGTGATTA' /data/testR1.fastq.gz /data/testR2.fastq.gz

Help

See the following for usage:

OVERVIEW

The fqgrep utility searches any given input FASTQ files, selecting records whose bases match one or more patterns.  By default, a pattern matches the bases in a FASTQ record if the regular expression (RE) in the pattern matches the bases.  An empty expression matches every line.  Each FASTQ record that matches at least one of the patterns is written to the standard output.

INPUT COMPRESSION

By default, the input files are assumed to be uncompressed with the following exceptions: (1) If the input files are real files and end with .gz or .bgz, they are assumed to be GZIP compressed, or (2) if they end with .fastq or .fq, they are assumed to be uncompressed, or (3) if the -Z/--decompress option is specified then any unrecongized inputs (including standard input) are assumed to be GZIP compressed.

THREADS

The --threads option controls the number of threads used to search the reads. Independently, for single end reads or interleaved paired end reads, a single thread will be used to read each input FASTQ.  For paired end reads across pairs of FASTQs, two threads will be used to read the FASTQs for each end of a pair.  Finally, a single thread will be created for the writer.

EXIT STATUS

The fqgrep utility exits with one of the following values: 0 if one or more lines were selected, 1 if no lines were selected, and >1 if an error occurred.

Usage: fqgrep [OPTIONS] [ARGS]...

Arguments:
  [ARGS]...
          The first argument is the pattern to match, with the remaining arguments containing the files to match.  If -e is given, then all the arguments are files to match. Use standard input if either no files are given or - is given

Options:
  -t, --threads <THREADS>
          The number of threads to use for matching reads against pattern.  See the full usage for threads specific to reading and writing
          
          [default: 10]

      --color <COLOR>
          Mark up the matching text.  The possible values of when are “never”, “always” and “auto”
          
          [default: never]
          [possible values: never, always, auto]

  -c, --count
          Only a count of selected lines is written to standard output

  -e, --regexp <REGEXP>
          Specify a pattern used during the search of the input: an input line is selected if it matches any of the specified patterns.  This option is most useful when multiple -e options are used to specify multiple patterns

  -F, --fixed-strings
          Interpret pattern as a set of fixed strings

  -f, --file <FILE>
          Read one or more newline separated patterns from file.  Empty pattern lines match every input line.  Newlines are not considered part of a pattern.  If file is empty, nothing is matched

  -N, --read-names-file <READ_NAMES_FILE>
          Read one or more newline separated query names (read IDs) from file.  Records whose read ID (the portion of the header before the first whitespace) exactly matches any query name in the file will be selected.  This option is mutually exclusive with pattern matching options (-e, -f, -F, and positional pattern)

  -v
          Selected lines are those not matching any of the specified patterns

  -Z, --decompress
          Assume all unrecognized inputs are GZIP compressed

      --paired
          Treat the input files as paired.  The number of input files must be a multiple of two, with the first file being R1, second R2, third R1, fourth R2, and so on.  If the pattern matches either R1 or R2, then both R1 and R2 will be output (interleaved).  If the input is standard input, then treat the input as interlaved paired end reads

      --no-order
          Do not preserve input order in output.  By default, output records are written in the same order as the input, even when using multiple threads.  This option disables the reorder buffer, which may slightly reduce memory usage at the cost of non-deterministic output order

      --reverse-complement
          Search the reverse complement for matches

      --progress
          Write progress information

      --protein
          The input files contain protein sequences (amino acids), not DNA sequences

      --iupac <IUPAC>
          Determine if IUPAC codes should be treated specially when -F/--fixed-strings is specified.  If Never is given, patterns are left as-is.  If Expand is given, then the pattern (or patterns) will be replaced with fixed strings without IUPAC codes, for example, GATK will be expanded to two fixed patterns GATG and GATT.  If Regex is given, then the pattern (or patterns) will be replaced with regular expressions without IUPAC codes, for example, GATK will be changed to the regular expression GAT[GT]. If BitMask is given, then the pattern (or patterns) will be matched using a 4-bit bitmask encoding where each IUPAC code is represented as the bitwise OR of its constituent bases (A=1, C=2, G=4, T=8)
          
          [default: never]
          [possible values: never, expand, regex, bit-mask]

  -h, --help
          Print help (see a summary with '-h')

  -V, --version
          Print version