Testing indexing FASTQ file with zero length record (issue #269)

Example file from Sam Hunter, included in his bug report.
Add ePrimer3 option -opttm which replaces -otm in EMBOSS 6.6.0

This is a squashed commit from pull request #271 (modified by PJC).
committed a patch from Anthony Mathelier to allow parsing the latest release of JASPAR
Add license statements to Bio.NMR files; Turn comments into docstrings
Add see also note for glob module to index_db functions
Download missing DTD files automatically and save them to a local directory
Only write to handle if we could open it
Only warn if something went wrong
Fixing a typo
Make sure all Entrez tests pass
Fix inconsistent tabs vs spaces (error under Python 3)
Updated some DTD files from NCBI
Warn when parsing BLAST XML files with duplicate hit IDs
Update blast-xml warning test for PyPy[2.2.1] compatibility
updating to avoid warnings with the latest version of numpy
add back off delay to qblast

previous delay was a constant 3 sec. Now the delay starts at 2sec and increases as follows: delay += .5*delay to a max of 120sec.
The approx. delay and total time is as follows;
(delay, total)(2, 2)
(delay, total)(3, 5)
(delay, total)(4, 9)
(delay, total)(6, 16)
(delay, total)(10, 26)
(delay, total)(15, 41)
(delay, total)(22, 64)
(delay, total)(34, 98)
(delay, total)(51, 149)
(delay, total)(76, 226)
(delay, total)(115, 341)
(delay, total)(120, 461)
Update NEWS file with major changes and contributors since Biopython 1.63
In the examples, use the code in Bio.motifs rather than Bio.Motif
GenomeDiagram tweak for Python 3 (using py33 ReportLab branch)

The forthcoming ReportLab v3 release will natively support
Python 2.7 and 3.3 onwards. This work is currently available
as the py33 branch on their BitBucket repository, which I
used to test this simple string change (bytes versus unicode).
Python 3 fix for ColorSpiral test: sort dictionary entries