NAME
FASTX::Seq - A class for representing a sequence for FASTX::Reader
VERSION
version 1.12.0
SYNOPSIS
A sequence object supported from FASTX::Reader structured as a BioX::Seq record, but keeping the attribute names as the scalar natively provided by FASTX::Reader. Order of arguments matters:
- seq
-
The actual sequence, the only mandatory field (string)
- name
-
The sequence identifier, can be omitted (string / undef)
- comment
-
The sequence comment, can be omitted (string / undef)
- qual
-
The sequence quality, if provided its length must match the sequence one (string / undef)
use FASTX::Seq;
my $fastq = new($seq, $name, $comment, $qual);
my $fasta = new($seq, $name, $comment);
my $barseq = new("ATGC");
# Change attribute
$fastq->seq("ATGCTT");GLOBAL VARIABLES
$FASTX::Seq::DEFAULT_QUALITY [default: 'I']
Default quality character to use when no quality is provided. Stored in each record as default_quality.
$FASTX::Seq::DEFAULT_LINE_LEN [default: 0]
Default line length for FASTA output. If set to 0, no line break is added. Stored in each record as line_len.
$FASTX::Seq::DEFAULT_OFFSET [default: 33]
Default quality offset. Default is 33, which is the standard for Sanger/Illumina 1.8+. Stored in each record as offset.
NAME
FASTX::Seq - A class for representing a sequence for FASTX::Reader
VERSION
version 1.11.0
MAIN METHODS
new($seq, $name, $comment, $qual)
Create a new instance of FASTX::Seq. The sequence is the only required field.
Positional arguments (order matters, only the first is mandatory, but comment must be undef if qual is not provided):
my $record = FASTX::Seq->new($seq, $name, $comment, $qual);Named arguments (order does not matter, only -seq is mandatory, other can be omitted):
my $fastq_record = FASTX::Seq->new(
-seq => "CACCA", # -sequence is also valid
-name => $name, # -id is also valid
-comment => $comment,
-qual => "IFIGH", # -quality is also valid
-offset => 33,
-line_len => $line_len,
-default_quality => $default_quality,
);copy()
Create a copy of the current instance.
my $copy = $fastq->copy();seq()
Get or update the sequence field.
my $seq = $fastq->seq();
$fastq->seq("ATGCTT");name()
Get or update the sequence field.
my $seq = $fastq->name();
$fastq->name("seq1");qual()
Get or update the sequence field.
my $seq = $fastq->qual();
$fastq->qual("IIIII");comment()
Get or update the sequence field.
my $seq = $fastq->comment();
$fastq->comment("len=" . length($fastq->seq()));offset()
Get or update the sequence field.
$fastq->offset(33);line_len()
Get or update the sequence field.
$fastq->line_len(33);default_quality()
Get or update the sequence field.
$fastq->default_quality(33);len()
Length of the sequence
my $len = $fastq->len();SEQUENCE MANIPULATION
rev()
Reverse (no complement) the sequence in place.
my $rev = $fastq->rev();rc()
Reverse and complement the sequence in place (as it's revesible). Supports IUPAC degenerate bases.
my $rc = $fastq->rc();slice()
Retrieve a slice of the sequence (from, length), as perl's substr. The change is not in place, will return a new object.
my $slice = $fastq->slice(0, 200);translate([genetic_code])
Return the sequence as translated protein sequence. Optional artument is the NCBI Genetic code:
my $seq = FASTX::Seq->new(
-seq => 'ATGATG',
-id => 'seq1',
);
my $orf = $seq->translate(11);
say $orf->seq();QUALITY
char2qual(char, [offset]])
Convert encoded quality to its integer value. If offset is not provided, will use the default offset.
my $encoded_phred = $fastq->qual2phred("!", 33);qual2char(int, [offset])
Convert integer quality score to encoded phred scores. If offset is not provided, will use the default offset.
my $encoded_phred = $fastq->qual2phred("!", 33);qualities()
Returns an array of quality values for each base of the record.
my @qualities = $fastq->qualities();min_qual()
Return the lowest quality score in the record.
my @qualities = $fastq->min_qual();max_qual()
Return the lowest quality score in the record.
my @qualities = $fastq->max_qual();trim_after(quality_integer)
Trim the record in place after the first base with a quality score lower or equal than the provided integer.
$fastq->trim_after(20);trim_until(quality_integer)
Trim the record in place up to the the first base with a quality score higher or equal than the provided integer.
$fastq->trim_until(20);VALIDATION AND STRING GENERATION
string()
Return the sequence as a string. If arguments are provided, they will be treated as FASTA or FASTQ specific according to the record format.
print $seq->string();as_string()
Alias to string()
asfasta([length]])
Return the sequence as a FASTA string. If the length is provided, the sequence will be split into lines of that length.
my $fasta = $seq->asfasta();asfastq()
Return the sequence as a FASTQ string. Will use a dummy fixed value quality if the sequence didnt have a quality string. Provide an character to use it as quality value, will override the record quality, if it has one.
my $fasta = $seq->asfastq();as_fasta()
Alias to asfasta()
as_fastq()
Alias to asfastq()
is_fasta()
Return true if the record has not a quality value stored (FASTA)
if ( $seq->is_fasta() ) {
...
}is_fastq()
Return true if the record has a quality value stored (FASTQ)
if ( $seq->is_fastq() ) {
...
}AUTHOR
Andrea Telatin <andrea@telatin.com>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2019 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) LicenseAUTHOR
Andrea Telatin <andrea@telatin.com>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2019 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License