Set it up so that we can give default, minimum and maximum values to all the numeric parameters for the cleaning functions by editing the file "ranges.txt" in the CIAlign/CIAlign folder. This is just for us to use, not the users - so we can set the range of values which are valid. When we change them the --help and the range which the program will accept will automatically update. I also set up the manual to automatically include these by running the update_manual.py script - which replaces the old update_manual.sh script. Instead of updating user_guide.md we should now update user_guide_template.md.
Moved all the argument parser stuff from CIAlign.py to a separate file - argP.py
Moved the code to actually run CIAlign from CIAlign.py to runCIAlign.py and split it up into functions, added extra comments and docstrings, generally tidied it up a bit
Fixed a couple of small errors with the testing - I think these were just due to differences between our machines
Instead of checking the images for the mini alignments are identical it now checks that they are highly similar - because there were minor differences in the rendering between the test image and the one I made - different shades of the same colour or tiny differences in where the borders of the colours are.
The tests for cropSeq.py were raising the warning you added in 195f043 so I made mingap_perc for the tests a bit bigger and some of the sequences a bit longer - please check it's still testing what you wanted it to test.
the listFonts function was raising a few "glyph error" warnings on my computer - I just made it skip the fonts that cause these warnings
The other commits to testing are just me fixing stuff I broke while I was doing the above
Added an option to the miniAlignments to keep the numbering from the initial alignment in the mini alignment for the output (e.g. if the input is 1, 2, 3, 4 and 3 is removed the rows in the output will be numbered 1, 2, 4 rather than 1, 2, 3.
Hi Lotti,
I have:
Set it up so that we can give default, minimum and maximum values to all the numeric parameters for the cleaning functions by editing the file "ranges.txt" in the CIAlign/CIAlign folder. This is just for us to use, not the users - so we can set the range of values which are valid. When we change them the --help and the range which the program will accept will automatically update. I also set up the manual to automatically include these by running the update_manual.py script - which replaces the old update_manual.sh script. Instead of updating user_guide.md we should now update user_guide_template.md.
Moved all the argument parser stuff from CIAlign.py to a separate file - argP.py
Moved the code to actually run CIAlign from CIAlign.py to runCIAlign.py and split it up into functions, added extra comments and docstrings, generally tidied it up a bit
Fixed a couple of small errors with the testing - I think these were just due to differences between our machines
Added an option to the miniAlignments to keep the numbering from the initial alignment in the mini alignment for the output (e.g. if the input is 1, 2, 3, 4 and 3 is removed the rows in the output will be numbered 1, 2, 4 rather than 1, 2, 3.
Please merge this in if it's all OK with you!
Katy