widdowquinn
commented
9 years ago Hi Pete,
You may like to try using the pyani module instead - it has improvements and bug fixes that make it a better option than the calculate_ani.py script, and the average_nucleotide_identity.py script that comes with it works very similarly to calculate_ani.py.
Regarding your query, the reason there's a KeyError is probably that one or more of the alignments comes up with a 0% alignment, and the script doesn't like that. This bug is (I believe) eliminated in the pyani module.
I should really deprecate this script, now that pyani is nearly finished.
EDIT: here's the link to the pyani repo: https://github.com/widdowquinn/pyani
L.
I installed biopython on my mac to run this script, and it seems to be starting up just fine. I don't have rpy2, so that is the source of my first error message. The next issue is unclear to me: the following is displayed, then the program quits before finishing the alb_lengths.tab table. That table contains only column labels and not rows.
Could not import rpy2: graphical output and TETRA method not available Traceback (most recent call last): File "/Users/peternewell/Bioinformatics/Teaching-0.1.0/Comparative_Genomics_and_Visualisation/Part_1/scripts/calculate_ani.py", line 1088, in
methods[options.method]()
File "/Users/peternewell/Bioinformatics/Teaching-0.1.0/Comparative_Genomics_and_Visualisation/Part_1/scripts/calculate_ani.py", line 293, in calculate_anim
"Aligment lengths")
File "/Users/peternewell/Bioinformatics/Teaching-0.1.0/Comparative_Genomics_and_Visualisation/Part_1/scripts/calculate_ani.py", line 647, in write_table
val = values[(n2, n1)]
KeyError: ('amac', 'aaat')
'amac' and 'aaat' are names of my config files.
Any insights would be greatly appreciated.