Consider this Beta until it is officially released on CPAN. I want to solicit community feedback before freezing the API.

NAME

Bio::IRCF::FASTQ::Tiny

VERSION

version 0.028

SYNOPSIS

use v5.10;
use strict;
use warnings;
use autodie;

use Bio::IRCF::FASTQ::Tiny qw( process_fastq );

my $fastq_filename = shift;

open(my $fh_fastq, '<', $fastq_filename);

my $make_fasta_coderef = sub {
    my $entry_href = shift // return; # Explicit return for undefined value

    say '>' . $entry_href->{header};
    say $entry_href->{seq}         ;
    return 1; # Must return true value
};

process_fastq($fh_fastq, $make_fasta_coderef);

Another example. This one keeps track of each sequence and how many times it occurs in a FASTQ file.

use v5.10;
use strict;
use warnings;
use autodie;

use Bio::IRCF::FASTQ::Tiny qw( iterator );

my $fastq_filename = shift;

my $get_simple_entry = sub { return shift(); };

my $fastq_it = iterator($fastq_filename, $get_simple_entry);

my %count_of;

while(my $entry_href = $fastq_it->() ){

    my $sequence = $entry_href->{seq};

    $count_of{ $sequence }++;
}

# Print out list of sequences and how many times each occurred
for my $sequence ( sort keys %count_of){
   say $sequence, "\t", $count_of{$sequence};
}

DESCRIPTION

SUBROUTINES/METHODS

iterator

    positional parameters:
        file name
            This is the name of a FASTQ file.

        coderef (optional)

            For each iteration, this coderef will be passed a hashref
            containing the keys 'header','seq','q_header', and 'qual',
            which refer to strings containing the header, sequence,
            quality header, and quality scores of a FASTQ entry,
            respectively. The strings for the header and quality header
            are stripped of their first character (i.e. '@' and '+',
            respectively).

            If no coderef is specified, this will simply return the
            hashref described above.

Returns an iterator which applies the coderef to one FASTQ entry at a
time, returning the result.

process_fastq

Takes the same arguments as iterator. However, instead of returning
an iterator, it builds one internally and then exhaustively applies it to
every entry in the FASTQ file.

coderef_print_altered_quality

positional parameters:
    filehandle
        Output filehandle to which the altered FASTQ file will be written.

    integer
        Value added to the ASCII value of each quality character. For
        example, if this is -31, then a score of 'B' becomes '#', changing
        from an "old Illumina" encoding to the Sanger encoding.

Returns a coderef compatible with C<process_fastq> or C<iterator>.

coderef_print_barcoded_entry

positional parameters:

    hashref with the following keys

        fh_out  Filehandle to print to.
        barcodes  String containing barcodes separated by whitespace.

Returns a coderef compatible with C<process_fastq> or C<iterator>.

coderef_print_entry

Returns a coderef compatible with C<process_fastq> or C<iterator>.

open_input

positional parameter: 

    filename (if last extension is 'gz', uses IO::Uncompress::Gunzip)

Returns a readable filehandle

open_output

positional parameter: 

    filename (if last extension is 'gz', uses IO::Compress::Gzip)

Returns a writable filehandle

RATIONALE

Speed and flexibility. To change quality score formats, for example, this
is over 10x faster than using BioPerl.

DIAGNOSTICS

CONFIGURATION AND ENVIRONMENT

None special, besides those described in DEPENDENCIES.

DEPENDENCIES

Perl 5.10 or later

Core Perl modules if not installed (e.g. on RedHat install "perl-core")
    IO::Compress::Gzip
    IO::Uncompress::Gunzip

Tests require 
    File::Slurp

INCOMPATIBILITIES

None that the author is aware of.

BUGS AND LIMITATIONS

 There are no known bugs in this module.

 Please report problems to molecules at cpan.org.

 Patches are welcome.

SEE ALSO

BioPerl

ACKNOWLEDGEMENTS

Utilities (in bin directory)

extract_singletons_from_paired_fastq

SYNOPSIS

extract_singletons_from_paired_fastq A_R1.fastq A_R2.fastq

DESCRIPTION

Given two FASTQ files (e.g. A_R1.fastq.gz and A_R2.fastq.gz), outputs the following:

• A_R1.good_paired.fastq.gz the original A_R1.fastq.gz file except that records have been removed for "orphans" and "empty" or "too short" sequences.
• A_R2.good_paired.fastq.gz the original A_R2.fastq.gz file except that records have been removed for "orphans" and "empty" or "too short" sequences.
• A_R1.orphans.fastq.gz sequences from A_R1.fastq.gz that lost its pair from A_R2.fastq.gz
• A_R2.orphans.fastq.gz sequences from A_R2.fastq.gz that lost its pair from A_R1.fastq.gz

extract_internally_barcoded_fastq

SYNOPSIS

extract_internally_barcoded_fastq A_R1.fastq.gz barcodes.txt 

DESCRIPTION

Given a FASTQ file and a file containing a list of 5' barcodes, output one FASTQ file containing sequences for each barcode.

FASTQ_Hash

DESCRIPTION

calculate an MD5sum specific to the records in one or more FASTQ files, but is independent of the order they appear. (Warning: This won't help you if the order of sequences in your files is important, such as ensuring that paired read files are always in a particular order.).