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NAME

fu-grep - Extract sequences using patterns from FASTA/FASTQ files

SYNOPSIS

fu-grep [options] Pattern InputFile.fa [...]

DESCRIPTION

fu-grep is a versatile tool for searching and extracting sequences from FASTA/FASTQ files based on various criteria. It can search for patterns in:

  • DNA sequences (including reverse complement)
  • Sequence names
  • Sequence comments

The tool supports both stranded and unstranded searches, and can provide detailed annotations about the matches found.

OPTIONS

  • -a, --annotate

    Add comments to the sequence when match is found. The annotation includes:

    • Total number of matches
    • Number of forward matches
    • Number of reverse complement matches (unless --stranded is used)
    • Source filename (when processing multiple files)

  • -n, --name

    Search pattern in sequence name instead of the sequence itself

  • -c, --comments

    Search pattern in sequence comments instead of the sequence itself

  • -s, --stranded

    Do not search for reverse complemented oligo

  • -f, --fasta

    Force output in FASTA format, even for FASTQ input

  • --cs, --comment-separator STR

    Specify custom comment separator (default: tab)

  • -v, --verbose

    Print verbose output

  • -d, --debug

    Print debug information

  • --version

    Print version information and exit

EXAMPLES

Search for a specific DNA pattern:

fu-grep AAGCTT input.fa > matched.fa

Search in multiple files with annotation:

fu-grep -a AAGCTT sample1.fa sample2.fa > matches.fa

Search in sequence names:

fu-grep -n "gene" sequences.fa > named.fa

Process FASTQ file but output in FASTA format:

fu-grep -f AAGCTT input.fastq > output.fa

NOTES

The tool will automatically search for both forward and reverse complement sequences unless the --stranded option is used.

MODERN ALTERNATIVE

This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis. This suite is maintained for the higher portability of Perl scripts under certain circumstances.

SeqFu is available at https://github.com/telatin/seqfu2, and can be installed with BioConda conda install -c bioconda seqfu

CITING

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059