SYNOPSIS
################## pertains to FASTQ parsing only ##################
# grabs the FASTQ parser, specifies the Illumina variant
my $in = Bio::SeqIO->new(-format => 'fastq-illumina',
-file => 'mydata.fq');
# simple 'fastq' format defaults to 'sanger' variant
my $out = Bio::SeqIO->new(-format => 'fastq',
-file => '>mydata.fq');
# $seq is a Bio::Seq::Quality object
while (my $seq = $in->next_seq) {
$out->write_seq($seq); # convert Illumina 1.3 to Sanger format
}
# for 4x faster parsing, one can do something like this for raw data
use Bio::Seq::Quality;
# $data is a hash reference containing all arguments to be passed to
# the Bio::Seq::Quality constructor
while (my $data = $in->next_dataset) {
# process $data, such as trim, etc
my $seq = Bio::Seq::Quality->new(%$data);
# for now, write_seq only accepts Bio::Seq::Quality, but may be modified
# to allow raw hash references for speed
$out->write_seq($data);
}
DESCRIPTION
This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat file databases.FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data. A typical FASTQ entry takes the form:
@HCDPQ1D0501 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT..... +HCDPQ1D0501 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65.....
where:
@ = descriptor, followed by one or more sequence lines
+ = optional descriptor (if present, must match first one), followed by one or
more qual lines
When writing FASTQ output the redundant descriptor following the '+' is by default left off to save disk space. If needed, one can set the quality_header() flag in order for this to be printed.
FASTQ and Bio::Seq::Quality mapping
FASTQ files have sequence and quality data on single line or multiple lines, and the quality values are single-byte encoded. Data are mapped very simply to Bio::Seq::Quality instances:
Data Bio::Seq::Quality method
------------------------------------------------------------------------
first non-whitespace chars in descriptor id^
descriptor line desc^
sequence lines seq
quality qual*
FASTQ variant namespace
^ first nonwhitespace chars are id(), everything else after (to end of line)
is in desc()
* Converted to PHRED quality scores where applicable ('solexa')
FASTQ variants
This parser supports all variants of FASTQ, including Illumina v 1.0 and 1.3:
variant note
-----------------------------------------------------------
sanger original
solexa Solexa, Inc. (2004), aka Illumina 1.0
illumina Illumina 1.3
The variant can be specified by passing by either passing the additional -variant parameter to the constructor:
my $in = Bio::SeqIO->new(-format => 'fastq',
-variant => 'solexa',
-file => 'mysol.fq');
or by passing the format and variant together (Bio::SeqIO will now handle this and convert it accordingly to the proper argument):
my $in = Bio::SeqIO->new(-format => 'fastq-solexa',
-file => 'mysol.fq');
Variants can be converted back and forth from one another; however, due to the difference in scaling for solexa quality reads, converting from 'illumina' or 'sanger' FASTQ to solexa is not recommended.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHORS - Chris Fields (taken over from Tony Cox)
Email: cjfields at bioperl dot orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _Bio::SeqIO interface methods
next_seq
Title : next_seq Usage : $seq = $stream->next_seq() Function : returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE Status : Stable
write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function : writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq::Quality
Note : This now conforms to SeqIO spec (module output is same format as
next_seq)
Status : Stable
variant
Title : variant
Usage : $format = $obj->variant();
Function: Get and set method for the quality sequence variant. This is
important for indicating the encoding/decoding to be used for
quality data.
Current values accepted are:
'sanger' (orginal FASTQ)
ASCII encoding from 33-126, PHRED quality score from 0 to 93
'solexa' (aka illumina1.0)
ASCII encoding from 59-104, SOLEXA quality score from -5 to 40
'illumina' (aka illumina1.3)
ASCII encoding from 64-104, PHRED quality score from 0 to 40
(Derived from the MAQ website):
For 'solexa', scores are converted to PHRED qual scores using:
$Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10)
Returns : string
Args : new value, string
Plugin-specific methods
next_dataset
Title : next_dataset Usage : $obj->next_dataset Function : returns a hash reference containing the parsed data Returns : hash reference Args : none Status : Stable
write_fastq
Title : write_fastq Usage : $stream->write_fastq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq::Quality object Status : Deprecated (delegates to write_seq)
write_fasta
Title : write_fasta
Usage : $stream->write_fasta(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
Note : This method does not currently delegate to Bio::SeqIO::fasta
(maybe it should?). Not sure whether we should keep this as a
convenience method.
Status : Unstable
write_qual
Title : write_qual
Usage : $stream->write_qual(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq::Quality object
Note : This method does not currently delegate to Bio::SeqIO::qual
(maybe it should?). Not sure whether we should keep this as a
convenience method.
Status : Unstable
validate
Title : validate Usage : $obj->validate(0) Function : flag for format/qual range validation - default is 1, validate Returns : Bool (0/1) Args : Bool (0/1) Status : Stable (may be moved to interface)
quality_header
Title : quality_header Usage : $obj->quality_header Function : flag for printing quality header - default is 0, no header Returns : Bool (0/1) Args : Bool (0/1) Status : Unstable (name may change dep. on feedback)