[Biopython-dev] [Bug 2767] Bio.SeqIO support for FASTQ and QUAL files

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http://bugzilla.open-bio.org/show_bug.cgi?id=2767





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2009-02-19 12:42 EST -------
Created an attachment (id=1244)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1244&action=view)
Read/write support for FASTQ and QUAL files, using the annotation dict

This patch stores the PHRED qualities as a list of integers in the SeqRecord's
annotations dictionary.  Changing this to use say a property, or a separate
per-letter-annotation dictionary should be trivial.

For QUAL files, the SeqRecord's seq is set to None.  This requires a few
changes to test_SeqIO.py which does not expect this.  We could also consider
introducing an UnknownSeq object (giving it a character like "?", "N", or "X",
an alphabet, and a length).  This would have a __str__ output like "?"*length.


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