[Biopython-dev] Biopython 1.00a2 release

Iddo Friedberg idoerg at cc.huji.ac.il
Thu Jul 5 18:12:01 EDT 2001


On Thu, 5 Jul 2001, Brad Chapman wrote:

: Jeff:
: > test_FSSP is still failing the regression tests for me.It seems to
: > be caused by:
: > f.write("\nRecords filtered in %s\n" % sum_ge_15.keys())
: >
: > Since dictionaries are unordered, it is outputting them in a
: > different order than they did when the output was created.
: Ya, I also did this myself on some tests. It is very easy to get
: tricked on this (well, at least it was easy for me to get tricked :-)

Same here. Didn't know that, (though I should have thought about it).
Jeff's fix is fine. Thanks for taking the time to do this.

One more thing: can the following correction please be inserted in the

(Section 3.5.5)
Amend the paragraph beginning with "Qi - " to:

Qi - is automatically assigned to 0.05 for a protein alphabet, and 0.25
for a nucleic acid alphabet. This is for geting the information content
without any assumption of prior distribtions. When assuming priors, or
when using a non-standard alphabet, user should supply the values for Qi.

Scratch the whole paragraph (just following) about gap characters,
including the 2nd equation.  We're not doing it that way anyway.




Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |

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