Bio::SeqReader::FastqRecord - Class providing methods for representing header, sequence, and quality information in FASTQ records.
use Bio::SeqReader::FastqRecord;
my $so = new Bio::SeqReader::FastqRecord(); $so->seq( 'ACGTACGT' ); print $so->seq(); # ACGTACGT
Class representing a sequence in FASTQ format. Headers 1 and 2, sequence text, and quality text are accessed by the object's getter-setter methods.
Bio::SeqReader::FastqRecord provides no class methods.
Bio::SeqReader::FastqRecord provides the following instance methods.
Returns a new Bio::SeqReader::FastqRecord object.
# Void constructor my $so = new Bio::SeqReader::FastqRecord(); # Constructor with initial values my $so = new Bio::SeqReader::FastqRecord( header1 => 'R_12345 read info ...', seqtext => 'ACGTACGT', header2 => '', qualtext => 'A@AA?#??' );
Getter for the display id associated with a Bio::SeqReader::FastqRecord object. Makes use of the current contents of header 1.
print $so->display_id(); # => R_12345
Getter-setter for the first header text from a Bio::SeqReader::FastqRecord object.
$so->header1( 'R_12345 read info ...' ); print $so->header1(); # => R_12345 read info
Getter-setter for the second header text from a Bio::SeqReader::FastqRecord object.
$so->header2( 'second header info ...' ); print $so->header2(); # => second header info ...
Getter-setter for the quality text from a Bio::SeqReader::FastqRecord object.
$so->quals( 'A@AA?#??' ); print $so->quals(); # => A@AA?#??
Reset a Bio::SeqReader::FastqRecord object. Basically sets all internal data to empty strings.
Getter-setter for the sequence text from a Bio::SeqReader::FastqRecord object.
$so->seq( 'ACGTACGT' ); print $so->seq(); # => ACGTACGT
Perl core.
None reported yet, but let me know.
Bio::SeqReader::Fastq, Bio::SeqReader.
John A. Crow <jac_at_cpan_dot_org>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.
Copyright (C) 2012 by John A. Crow Copyright (C) 2012 by National Center for Genome Resources
To install Bio::SeqReader, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::SeqReader
CPAN shell
perl -MCPAN -e shell install Bio::SeqReader
For more information on module installation, please visit the detailed CPAN module installation guide.