Bio::SeqIO::fastq 1.4 review

Bio::SeqIO::fastq is a fastq sequence input/output stream. SYNOPSIS Do not use this module directly

License: Perl Artistic License File size: 4788K Developer: Tony Cox

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Bio::SeqIO::fastq is a fastq sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::SeqIO class.

This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases.

Fastq is a file format used frequently at the Sanger Centre to bundle a fasta sequence and its quality data. A typical fastaq entry takes the from:

@HCDPQ1D0501
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.....
+HCDPQ1D0501
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65.....

Fastq files have sequence and quality data on a single line and the quality values are single-byte encoded. To retrieve the decimal values for qualities you need to subtract 33 (or Octal 41) from each byte and then convert to a '2 digit + 1 space' integer. You can check if 33 is the right number because the first byte which is always '!' corresponds to a quality value of 0.

Requirements:
Perl