Consider this Beta until it is officially released on CPAN. I want to solicit community feedback before freezing the API.
Bio::IRCF::FASTQ::Tiny
version 0.028
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};
}
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.
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.
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>.
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>.
Returns a coderef compatible with C<process_fastq> or C<iterator>.
positional parameter:
filename (if last extension is 'gz', uses IO::Uncompress::Gunzip)
Returns a readable filehandle
positional parameter:
filename (if last extension is 'gz', uses IO::Compress::Gzip)
Returns a writable filehandle
Speed and flexibility. To change quality score formats, for example, this
is over 10x faster than using BioPerl.
None special, besides those described in 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
None that the author is aware of.
There are no known bugs in this module.
Please report problems to molecules at cpan.org.
Patches are welcome.
BioPerl
extract_singletons_from_paired_fastq A_R1.fastq A_R2.fastq
Given two FASTQ files (e.g. A_R1.fastq.gz and A_R2.fastq.gz), outputs the following:
A_R1.good_paired.fastq.gzthe originalA_R1.fastq.gzfile except that records have been removed for "orphans" and "empty" or "too short" sequences.A_R2.good_paired.fastq.gzthe originalA_R2.fastq.gzfile except that records have been removed for "orphans" and "empty" or "too short" sequences.A_R1.orphans.fastq.gzsequences fromA_R1.fastq.gzthat lost its pair fromA_R2.fastq.gzA_R2.orphans.fastq.gzsequences fromA_R2.fastq.gzthat lost its pair fromA_R1.fastq.gz
extract_internally_barcoded_fastq A_R1.fastq.gz barcodes.txt
Given a FASTQ file and a file containing a list of 5' barcodes, output one FASTQ file containing sequences for each barcode.
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.).