This is a small step towards targetting both Python 2 and 3 without needing to run 2to3.
In yet another twist, the latest version of Prank names its output files "*.best.nex", "*.best.fas", etc. instead of the established "*.2.nex" which the unittest expected. The unittest now checks for both extensions.
Old Prank output: PRANK: converting 'Quality/example.fasta' to 'temp with space.fas' New Prank output: ----------------- PRANK v.130820: ----------------- Input for the analysis - converting 'Quality/example.fasta' to 'temp with space.fas'
These options no longer exist in Prank. Instead, "no" is now the default, and -showxml and -showtree are available options.
…xternal tools. Having it in run_tests.py was changing the default encoding causing problems on Python 3 with special characters in plain text files
…ing list (cherry-picked from my app-exec3 branch)
…701 (1 July 2010)
…g in Prank's output
…RF/PIR) so don't use them in our unit test
…hon 3 to ensure we get the child handles in text mode
…assert_ method is deprecated in Python 2.7
…om Cymon Cox via Bug 2961)
…EP8. Added a few missing license statements too.
…ilenames with spaces
…sed command line wrappers (Bug 2822)
…of 16s) and check we can parse the NEXUS output (Bug 2815)
…cations then the full path to try to locate the tools.