# rORForise
Read-based gene coverage evaluation
### Menu - (rORForise -h):
```bash
Running rORForise
usage: rORForise.py [-h] -d DIRECTORY -g GENOMES [GENOMES ...] --gc_prob GC_PROB -f FRAGMENTATION_TYPES [FRAGMENTATION_TYPES ...] -s SUBGROUPS [SUBGROUPS ...] -m METHODS
[METHODS ...]
Process genome evaluation parameters.
options:
-h, --help show this help message and exit
-d DIRECTORY, --directory DIRECTORY
Path to the main directory containing genome processing subdirectories.
-g GENOMES [GENOMES ...], --genomes GENOMES [GENOMES ...]
List of genome names to process. Example: 'Mycoplasma_genitalium_G37 Staphylococcus_aureus_502A'
--gc_prob GC_PROB GC probability of the genome being processed (e.g., 0.3169 for Mycoplasma genitalium).
-f FRAGMENTATION_TYPES [FRAGMENTATION_TYPES ...], --fragmentation_types FRAGMENTATION_TYPES [FRAGMENTATION_TYPES ...]
List of fragmentation types to use (e.g., 'ART_errFree').
-s SUBGROUPS [SUBGROUPS ...], --subgroups SUBGROUPS [SUBGROUPS ...]
List of subgroups for evaluation (e.g., 'Combined').
-m METHODS [METHODS ...], --methods METHODS [METHODS ...]
List of methods for evaluation (e.g., 'FragGeneScan').
```
## Example Run:
```bash
rORForise -d "../../Genome_Processing" -g "Mycoplasma_genitalium_G37" -f "ART_errFree" -s "Combined" -m "FragGeneScan" --gc_prob 0.3169
```
```bash
Running rORForise
Mycoplasma_genitalium_G37
FragGeneScan
ART_errFree
../../Genome_Processing/Mycoplasma_genitalium_G37/FragGeneScan *_ART_errFree_Combined.gff.gz ['../../Genome_Processing/Mycoplasma_genitalium_G37/FragGeneScan/FragGeneScan_ART_errFree_Combined.gff.gz']
../../Genome_Processing/Mycoplasma_genitalium_G37/FragGeneScan/FragGeneScan_ART_errFree_Combined.gff.gz
Number of predictions made for reads 69709
Number of CDS-aligned reads 70073
Number of CDS-aligned reads without predictions 5929
Number of CDS-aligned reads with at least one pred 64440
Number of predictions 69430
Number of on-target preds 64695
correct start 1211
correct stop 2030
correct frame 57249
correct direction 60168
incorrect stop 13624
incorrect start 8015
incorrect frame 2919
incorrect direction 4527
prediction ends before cds starts 660
prediction starts after cds ends 713
alternative start 1837
middle or alternative start 1913
alternative stop 5201
middle or alternative stop 1166
middle 49700
... Below is the output of the Codon predictions ...
```
Raw data
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