grepfasta.pl - Get entries from FASTA formatted file based on search in header
grepfasta.pl [options] -p 'pattern' file
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.
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-h, -?, --help
Print a brief help message and exits.
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-m, --man
Prints the manual page and exits.
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-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).
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-f, --search-file=file
Supply a search file with search strings.
Put several search strings on separate lines.
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-i, --inverse|-v
Inverse the output, i.e., print all fasta entries except the matching.
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--max=integer|-n
Maximum number of sequences to print. Default: all matches.
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-d, --debug
Do some debug printing.
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-V, --version
Print version.
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
Uses Perl modules Getopt::Long and Pod::Usage for documentation, and gzip/bzip2 for uncompressing.
Written by Johan A. A. Nylander
Copyright (c) 2009-2024 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.