- AUTHORS - Tony Cox
Bio::SeqIO::fastq - fastq sequence input/output stream
Do not use this module directly. Use it via the Bio::SeqIO class.
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 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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE
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 or Bio::Seq object
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
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