NAME

fu-extract - Get sequences by name (also using lists)

VERSION

version 1.5.0

PARAMETERS

• -p, --pattern PATTERN

  Print only sequences containing the given pattern in their name

• -l, --list FILE

  Print only sequences in the given list file (full name must match)

• -c, --column COLUMN

  In the list file, consider the name as the column COLUMN (default: 1)

• -h, --header CHAR

  Ignore lines starting with CHAR in the list (default: "#")

• -s, --separator CHAR

  Split the lines in the list file by CHAR (default: "\\t")

• -i, --case-insensitive

  Ignore case in the name (works both with -p and -l)

• -m, --minlen MINLEN

  Print only sequences with a length greater than MINLEN

• -x, --maxlen MAXLEN

  Print only sequences with a length less than MAXLEN

• -v, --verbose

  Print more information

EXAMPLES

Search by sequence name:

fu-extract -p 'BamHI' test.fa

Use a list to extract sequences:

fu-extract -l list.txt test.Fasta

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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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