NAME

fu-grep - Extract sequences using patterns

VERSION

version 1.5.0

USAGE

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

PARAMETERS

• -a, --annotate

  Add comments to the sequence when match is found

• n, --name

  Search pattern in sequence name (default: sequence)

• c, --comments

  Search pattern in sequence comments (default: sequence)

• s, --stranded

  Do not search reverse complemented oligo

• f, --fasta

  Force output in FASTA format

EXAMPLES

fu-grep DNASTRING test.fa test2.fa > matched.fa

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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

AUTHOR

Andrea Telatin andrea@telatin.com

COPYRIGHT AND LICENSE

This software is Copyright (c) 2018-2022 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License