This folder contains an example input which serves to:
- Demonstrate the usage of ProtHint
- To test whether the program is correctly configured
The example input genome comprises of the first 3 Mbp in Drosophila melanogaster's 2L chromosome.
To run ProtHint, use the following command
../bin/prothint.py input/genome.fasta input/proteins.fasta --geneSeeds input/genemark.gtf --workdir test
If everything is configured correctly, the results in the test folder should
match the contents of the output folder. Note that the order of hints in gff
files might differ.
To check, use for example:
diff <(sort test/prothint.gff) <(sort output/prothint.gff)
diff <(sort test/evidence.gff) <(sort output/evidence.gff)
The expected runtime for this example on a system with 8 CPUs (each 2.40GHz) and 8GB of RAM is about 1.5 minutes.