mcl package tests
Hi all,
in order to test the package mcl, I am using an approach as described on
the paper of Lima-Mendez et al. (DOI: 10.1093/molbev/msn023) method of
clustering of bacteriophages based on gene shared content.
I based mine on some modifications of an original implementation by
Ksenia Arkhipova. I have already pushed some files to the master but I
expect this to take another day or so.
Right now I have one blockage: I am doing a 3-step process
1. Using the package prodigal to generate a database file
2. Using awk to filter this
3. Using mcl to generate protein families
4. Using a custom python script to do pairwise comparisons
5. Out of the files generated in the previous step, I am using mcl again
to build clusters of genomes.
On that I have the following question:
- In order to complete step 5 I need to process a file generated from
step 3, using the custom, Python script. Now, as we discussed before, I
expect I can leave the script in (it's already on master) in order to
document this but is it a right approach to have prepared a test file
that is supposed to come out of a previous test result? That means I
expect that the previous test result has been successful!
Let me know if that makes sense.
p.s. Andreas: I don't need to include the testing files anymore, as I am
creating my own, user tests as described above.
Thanks
SH
Reply to: