Python 2.7 is required!
- Install virtualenv (if not already installed) via the following command:
pip2 install virtualenv
- Create a virtual environment called 'g4h_venv' via the following command:
virtualenv --python=python2.7 g4h_venv
- Activate the virtualenv via the following command:
. ./g4h_venv/bin/activate
- Install the G4hunter required packges in the virtualenv via the following command:
pip2 install -r requirements.txt
- Create the following directory structures
input
├── Gorilla_gorilla
├── Homo_sapiens
├── Pan_paniscus
├── Pan_troglodytes
├── Pongo_abelii
├── Pongo_pygmaeus
├── Symphalangus_syndactylus
output
├── Gorilla_gorilla
├── Homo_sapiens
├── Pan_paniscus
├── Pan_troglodytes
├── Pongo_abelii
├── Pongo_pygmaeus
├── Symphalangus_syndactylus
-
For each species, copy the fasta files (one for each chromosome) to the appropriate folder. Fasta files should be named chr1.fasta, ..., chr22.fatsa, chrX.fasta, and chrY.fasta.
-
Run G4Hunter for all species and all chromosomes via the following command:
./scripts/run_g4hunter_primates.sh
This shell script calls ./scripts/G4Hunter.py for for all species and all chromosomes in the ./input folder. The output files are written to the corresponding ./output folder. ./scripts/run_g4hunter_primates.sh takes 6 optional command line parameters, that can be overriden.
a. Window size (defaults to 25)
b. G4Hunter score (defaults to 1.5)
c. Species (deaults to "Gorilla_gorilla Pan_troglodytes Symphalangus_syndactylus Homo_sapiens Pongo_abelii Pan_paniscus Pongo_pygmaeus")
d. Chromosomes (defaults to "1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 X Y")
e. Input folder (defaults to "./input")
f. Output folder (defaults to "./output")
For each species and each chromosome, 2 output files are created. For eaxmple, for Gorilla_gorilla, chromosome 6, window size 25, and G4Hunter score 1.5, we get the following 2 files:
chr6-W25-S1.5-Merged.txt
chr6-W25-S1.5.bed