cplot, not cplot2
os.system to subprocess and PEP8
require a Shell (because of Windows)
Update test_SeqIO_online.py for NCBI GenBank change

pass "gbwithparts" instead of "gb" as rettype to Entrez
for GI:16130152, forcing Entrez to return the complete
genbank record. This record was recently to omit the
protein sequence when queried with rettype="gb".
Thank Phillip in NEWS file
universal new lines and shell not on win32
Fix corner case where EMBOSS_ROOT does not exist.

Previously we would try 'del name' where 'name' was undefined.
I'm also adding a new explicit error message when the EMBOSS
installation is broken ( not pointing at folder).

Also catch corner case where embossversion could return nothing.

Also try to cope if there is a space in the EMBOSS path (although
EMBOSS itself doesn't recommend this and it doesn't seem to work).
Quote/escape program names if they contain spaces.

I've tested this under Mac OS X using test_Clustalw_open.py
with a hack to set clustalw_exe to point at a copy of the
binary placed in a folder with spaces in the name.

I've tried testing this under Windows using EMBOSS but here
EMBOSS itself breaks if installed to a folder with spaces.
The new example in the docstring is therefore potentially
misleading.

Instead testing with ClustalW again, it seems Windows XP
itself must handle this as a special case - this works
(new Biopython wrapper behaviour):

"C:\Program Files\ClustalW2\clustalw2.exe" -infile=Registry/seqs.fasta -align -outfile=temp_test.aln -newtree=temp_test.dnd

However this worked too (old Biopython wrapper behaviour):

C:\Program Files\ClustalW2\clustalw2.exe -infile=Registry/seqs.fasta -align -outfile=temp_test.aln -newtree=temp_test.dnd

This suggests this fix isn't actually needed under Windows XP,
but is essential under Linux/Unix/Mac OS X whenever there are
spaces in binary's path.
Update MUSCLE doctest in line with new behaviour
Further test updates due to escaping change
Merge remote-tracking branch 'upstream/master' into samtools_wrapper