Creating Test Cases with RDP4.101 #117
Description
Logging this so we have a log of how the test cases were made:
Downloaded RDP4.101 from: http://web.cbio.uct.ac.za/~darren/rdp.html, as stated on the RDP4 publication
All test cases are currently in dev, under tests/rdp4. It includes the fasta file, as well as a csv file with the same name. The csv file is RDP4 output of that fasta file. If there is no csv file, that means RDP4 reported no hits. Additionally, all test files were made with the default parameters in RDP4, while running the Do a full exploratory recombination scan using all methods selected in the general options tab setting, which is all the methods
I added a few tests:
- no_recombinants.fa: 100 sequences, 9000 nucleotides each, made with pyvolve following REMASTER BDSIR tree
- 10recombs.fa: same as above, but with 10 breakpoints through the same pipeline as the recombr0 project (split_tree and then concatenating)
- 100recombs.fa: same as above, but 100
- pyvolve.fa: same as no_recombinants.fa, but only 10 sequences
- remaster_norecomb.fa: 10 sequences, 10000 nucleotides, direct output from REMASTER BDSIR sim
- simpleAG.fa: 4 sequnces of 200 NT each. One of all A, one of all G, one of 50A 100G 50A, and one of the inverse
- hiv_1_pol.fa: 4 random POL sequences of HIV-1 from NCBI
TODO:
- write script to parse csv outputs of RDP4 so we can compare openRDP
- finalize some unittests with some range of error that we are willing to accept to compare p-value and breakpoint indexes
- test openRDP methods on non-base parameters