NAME
Proch::Seqfu - SeqFu utilities
VERSION
version 1.7.0
SYNOPSIS
use Proch::Seqfu;
# Check if sequence is valid
my $is_valid = is_seq('ACGTACGT'); # returns 1
# Get reverse complement
my $rc = rc('ACGTACGT'); # returns 'ACGTACGT'
# Print sequences in FASTA format
fu_printfasta('seq1', 'sample sequence', 'ACGTACGT');
# Print sequences in FASTQ format
fu_printfastq('seq1', 'sample sequence', 'ACGTACGT', 'FFFFFFFF');DESCRIPTION
This module provides utilities for manipulating and formatting DNA/RNA sequences, with support for FASTA and FASTQ formats. It also includes functionality to interact with the SeqFu command-line tool.
FUNCTIONS
seqfu_version
my $version = seqfu_version();Returns the version of the installed SeqFu command-line tool. Returns a version string if SeqFu is installed and properly configured, -2 if there was an error executing the command, or a negative string for other errors.
has_seqfu
my $has_seqfu = has_seqfu();Checks if SeqFu is available in the system. Returns: 1 if SeqFu is available 0 if SeqFu is not available undef if the check failed
is_seq
my $valid = is_seq($sequence);Validates if a string contains only valid nucleotide characters (ACGTRYSWKMBDHVNU, case insensitive). Returns true if the sequence is valid, false otherwise.
rc
my $reverse_complement = rc($sequence);Generates the reverse complement of a DNA/RNA sequence. Handles both DNA and RNA (U/T) automatically. Returns undefined if the input sequence contains invalid characters.
verbose
verbose("Processing sequence...");Prints a message to STDERR if verbose mode is enabled ($fu_verbose is true). Messages are prefixed with " - ".
fu_printfasta
fu_printfasta($name, $comment, $sequence);Prints a sequence in FASTA format. The comment parameter is optional. Dies with an error message if: - name is undefined - sequence is undefined - sequence contains invalid characters
fu_printfastq
fu_printfastq($name, $comment, $sequence, $quality);Prints a sequence in FASTQ format. The comment parameter is optional. Dies with an error message if: - name is undefined - sequence is undefined - quality string is undefined - sequence contains invalid characters - sequence and quality lengths don't match
CONFIGURATION VARIABLES
- $fu_linesize
-
Controls the line width for sequence output. If set to 0 (default), sequences are printed without line breaks.
- $fu_verbose
-
Controls verbose output. Set to 1 to enable verbose messages, 0 to disable.
split_string
my $formatted = split_string($input_string);Splits a string into lines of length $fu_linesize. Returns the formatted string with line breaks.
AUTHOR
Andrea Telatin <andrea@telatin.com>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2018-2027 by Quadram Institute Bioscience.
This is free software, licensed under:
The MIT (X11) License