Bio::SeqIO::fastqBio::SeqIO::fastq is a fastq sequence input/output stream. | |
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Bio::SeqIO::fastq Ranking & Summary
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- License:
- Perl Artistic License
- Price:
- FREE
- Publisher Name:
- Tony Cox
- Publisher web site:
- http://search.cpan.org/~birney/bioperl-1.4/Bio/SeqIO/fastq.pm
Bio::SeqIO::fastq Tags
Bio::SeqIO::fastq Description
Bio::SeqIO::fastq is a fastq sequence input/output stream. Bio::SeqIO::fastq is a fastq sequence input/output stream.SYNOPSISDo 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 Requirements: · Perl
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