https://github.com/nylander/grepfasta

Yet another grep for FASTA formatted files - with regexp capacity!
https://github.com/nylander/grepfasta

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Yet another grep for FASTA formatted files - with regexp capacity!

• Host: GitHub
• URL: https://github.com/nylander/grepfasta
• Owner: nylander
• License: mit
• Created: 2012-12-18T16:17:42.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2020-03-24T21:55:38.000Z (about 6 years ago)
• Last Synced: 2023-03-24T03:25:13.397Z (about 3 years ago)
• Language: Perl
• Homepage:
• Size: 8.79 KB
• Stars: 3
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# NAME

grepfasta.pl - Get entries from FASTA formatted file based on search in header

# SYNOPSIS

    grepfasta.pl [options] -p 'pattern' file 

# DESCRIPTION

**grepfasta.pl** will search for the presence of _string_ in

the header of a FASTA entry, and print the entry to STDOUT if 

a match is found, or print all entries in the file except the

match (if **--inverse** is used).

The search pattern can be a regular expression (Perl), and can

be supplied on command line, or in a file.

If several patterns are given in the search file, all of them are

used for matching on all fasta entries.

The search is repeated for each fasta header in the file until EOF,

unless the **--max** option is used. The **--max** option only limits

the total number of sequences to print, which may be important

to consider if several search patterns are used in a search file.

The script can read compressed fasta files (.gz, .zip, .Z, .bz2),

if gzip and/or bunzip2 are available.

# OPTIONS

- **-h, -?, --help**

    Print a brief help message and exits.

- **-m, --man**

    Prints the manual page and exits.

- **-p, --search-pattern=**_string_

    Supply a search _string_.

    Put separated words (phrases) within single or double quotes (e.g., 'My query').

    Search string may be a regular expression (Perl).

- **-f, --search-file=**_file_

    Supply a search _file_ with search strings.

    Put several search strings on separate lines.

- **-i, --inverse|-v**

    Inverse the output, i.e., print all fasta entries except the matching. 

- **--max=_integer_|-n**

    Maximum number of sequences to print. Default: all matches.

- **-d, --debug**

    Do some debug printing.

- **-V, --version**

    Print version.

# USAGE

Examples:

    grepfasta.pl --search-pattern='ABC 12' data/file.fasta

    grepfasta.pl -p='ABC 12' data/file.fasta

    grepfasta.pl --search-file=data/search_file.txt data/file.fasta

    grepfasta.pl -f=data/search_file.txt data/file.fasta

    grepfasta.pl -p='ABC 12' --inverse data/file.fasta

    grepfasta.pl -p='ABC 12' -v data/file.fasta

    grepfasta.pl -p='ABC 12' data/file.fasta.gz

    grepfasta.pl -p='ABC 3' data/file.fasta

    grepfasta.pl -p='ABC 3' --max=1 data/file.fasta

    grepfasta.pl -p='ABC 1' data/file.fasta

    grepfasta.pl -p='1$' data/file.fasta

    grepfasta.pl -p='\w+\s+\d{2}$' data/file.fasta

    grepfasta.pl -p='[a-z]+\s+\d{2}$' data/file.fasta

    grepfasta.pl -p='^>[a-z]+\s+\d{2}$' data/file.fasta

# DEPENDENCIES

Uses Perl modules Getopt::Long and Pod::Usage for documentation,

and gzip/bzip2 for uncompressing.

# AUTHOR

Written by Johan A. A. Nylander

# LICENSE AND COPYRIGHT

Copyright (c) 2009-2023 Johan Nylander

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all

copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

SOFTWARE.

# DOWNLOAD

[https://github.com/nylander/grepfasta](https://github.com/nylander/grepfasta)