[Biopython-dev] [Bug 2865] Phd writer class for SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2865


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2009-08-21 09:55 EST -------
I've checked in a slightly revised version of Cymon's patch to allow
Bio.SeqIO to write "phd" files.

Checking in Tests/test_SeqIO_QualityIO.py;
/home/repository/biopython/biopython/Tests/test_SeqIO_QualityIO.py,v  <-- 
test_SeqIO_QualityIO.py
new revision: 1.14; previous revision: 1.13
done
Checking in Tests/output/test_SeqIO;
/home/repository/biopython/biopython/Tests/output/test_SeqIO,v  <--  test_SeqIO
new revision: 1.51; previous revision: 1.50
done
Checking in Bio/SeqIO/__init__.py;
/home/repository/biopython/biopython/Bio/SeqIO/__init__.py,v  <--  __init__.py
new revision: 1.58; previous revision: 1.57
done
Checking in Bio/SeqIO/PhdIO.py;
/home/repository/biopython/biopython/Bio/SeqIO/PhdIO.py,v  <--  PhdIO.py
new revision: 1.8; previous revision: 1.7
done

Cymon - could you double check this please? I made one change regarding
the filename/record description, and also you hadn't rounded the Solexa
scores to the nearest integer value after they were converted to PHRED
scores.

Peter


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