NAME

fu-grep - Extract sequences using patterns

VERSION

version 1.5.8

USAGE

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

PARAMETERS

-a, --annotate

Add comments to the sequence when match is found. This includes the number of matches (total, forward and reverse) and the file the sequence was found when more than one is parsed.

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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) 2018-2023 by Andrea Telatin.

This is free software, licensed under:

  The MIT (X11) License