File Coverage

blib/lib/Proch/Seqfu.pm

Criterion	Covered	Total	%
statement	32	59	54.2
branch	7	22	31.8
condition			n/a
subroutine	9	13	69.2
pod	8	8	100.0
total	56	102	54.9

package Proch::Seqfu;
#ABSTRACT: Helper module to support Seqfu tools

use 5.014;
use warnings;
use Carp qw(confess);
use Data::Dumper;
use Term::ANSIColor qw(:constants);
require Exporter;

$Proch::Seqfu::VERSION     = '1.6.1';
$Proch::Seqfu::fu_linesize = 0;
$Proch::Seqfu::fu_verbose  = 0;

our @ISA       = qw(Exporter);
our @EXPORT    = qw(rc fu_printfasta fu_printfastq verbose has_seqfu seqfu_version);
our @EXPORT_OK = qw($fu_linesize $fu_verbose);  # symbols to export on request


sub fu_printfasta {
    my ($name, $comment, $seq) = @_;
    my $print_comment = '';
    if (defined $comment) {
        $print_comment = ' ' . $comment;
    }

    say '>', $name, $print_comment;
    print split_string($seq);
}

sub fu_printfastq {
    my ($name, $comment, $seq, $qual) = @_;
    my $print_comment = '';
    if (defined $comment) {
        $print_comment = ' ' . $comment;
    }

    say '@', $name, $print_comment;
    print split_string($seq) , "+\n", split_string($qual);
}


# Print verbose info
sub verbose {
    if ($Proch::Seqfu::fu_verbose) {
        say STDERR " - ", $_[0];
    }
}


sub rc {
    my   $sequence = reverse($_[0]);
    if (is_seq($sequence)) {
        if ($sequence =~ /U/i) {
            $sequence =~ tr/ACGURYSWKMBDHVacguryswkmbdhv/UGCAYRSWMKVHDBugcayrswmkvhdb/;
        } else {
            $sequence =~ tr/ACGTRYSWKMBDHVacgtryswkmbdhv/TGCAYRSWMKVHDBtgcayrswmkvhdb/;
        }
        return $sequence;
    }
}


sub is_seq {
    my $string = $_[0];
    if ($string =~/[^ACGTRYSWKMBDHVNU]/i) {
        return 0;
    } else {
        return 1;
    }
}


sub split_string {
	my $input_string = $_[0];
	my $formatted = '';
	my $line_width = $Proch::Seqfu::fu_linesize; # change here
    return $input_string. "\n" unless ($line_width);
	for (my $i = 0; $i < length($input_string); $i += $line_width) {
		my $frag = substr($input_string, $i, $line_width);
		$formatted .= $frag."\n";
	}
	return $formatted;
}


sub seqfu_version {
    my $cmd = '';
    eval {
        $cmd = `seqfu version`;
    };
    chomp($cmd);
    if (length($@) > 0) {
        return -2;
    } elsif ($cmd =~/^(\d+)\.(\d+)\.?(\d+)?$/) {
        return $cmd;
    } else {
        return "-" . $cmd;
    }
}


sub has_seqfu {
    my $ver = seqfu_version();
    if (substr($ver, 0, 1) eq '-') {
        return 0
    } elsif (length($ver) > 0) {
        return 1
    } else {
        return undef;
    }
}
1;

=pod

=encoding UTF-8

=head1 NAME

Proch::Seqfu - Helper module to support Seqfu tools

=head1 VERSION

version 1.5.8

=head1 Proch::Seqfu

a legacy module for Seqfu utilities

=head2 fu_printfasta(name, comment, seq)

This function prints a sequence in fasta format

=head2 fu_printfastq(name, comment, seq, qual)

This function prints a sequence in FASTQ format

=head2 verbose(msg)

Print a text if $fu_verbose is set to 1

=head2 rc(dna)

Return the reverse complement of a string [degenerate base not supported]

=head2 is_seq(seq)

Check if a string is a DNA sequence, including degenerate chars.

=head2 split_string(dna)

Add newlines using $Proch::Seqfu::fu_linesize as line width

=head2 seqfu_version()

Check if a `seqfu` binary is present and returns its version if found.
Note this will require SeqFu > 1.13

=head2 has_seqfu()

If SeqFu is detected returns 1, 0 otherwise, I when detection of SeqFu version fails.

=head1 AUTHOR

Andrea Telatin

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2018-2023 by Andrea Telatin.

This is free software, licensed under:

  The MIT (X11) License

=cut

__END__