FASTX::Seq - A class for representing a sequence for FASTX::Reader
version 1.4.0
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.
FASTX::Reader
BioX::Seq
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");
Create a new instance of FASTX::Seq. The sequence is the only required field.
FASTX::Seq
Get or update the sequence field.
my $seq = $fastq->seq(); $fastq->seq("ATGCTT");
my $seq = $fastq->name(); $fastq->name("seq1");
my $seq = $fastq->qual(); $fastq->qual("IIIII");
my $seq = $fastq->comment(); $fastq->comment("len=" . length($fastq->seq()));
Reverse (no complement) the sequence.
my $rev = $fastq->rev();
Length of the sequence
my $len = $fastq->len();
Reverse and complement the sequence.
my $rc = $fastq->rc();
Return the sequence as a FASTA string.
my $fasta = $seq->asfasta();
Return the sequence as a FASTQ string. Will use a dummy fixed value quality if the sequence didnt have a quality string.
my $fasta = $seq->asfastq();
Andrea Telatin <andrea@telatin.com>
This software is Copyright (c) 2019 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License
To install FASTX::Reader, copy and paste the appropriate command in to your terminal.
cpanm
cpanm FASTX::Reader
CPAN shell
perl -MCPAN -e shell install FASTX::Reader
For more information on module installation, please visit the detailed CPAN module installation guide.