Download Latest Version RaFAH.pl (23.3 kB)
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Home / RaFAH_v0.1_Files
Name Modified Size InfoDownloads / Week
Parent folder
HP_Ranger_Model_3_Valid_Cols.txt 2020-09-08 954.4 kB
0
Predict_Host_RF.R 2020-09-08 1.3 kB
0
RaFAH_README.txt 2020-09-08 931 Bytes
0
RaFAH_v0.1.pl 2020-09-08 14.1 kB
0
RaFAH_v0.1_Ranger_Model.tgz 2020-09-08 73.1 MB
0
RaFAH_v0.1_hmm_models.tgz 2020-09-08 2.4 GB
0
Totals: 6 Items   2.5 GB 0 
Dependencies:

In order for RaFAH to work you will need the following dependencies installed:

BioPerl
Prodigal (v2.60)
HMMER (v3.1b2)
R (v3.6.3)
R libraries: ranger

Setup (These steps only need to be performed once):

To setup RaFAH download and decompress all the files listed in https://sourceforge.net/projects/rafah/files/RaFAH_v0.1_Files/

Next, open the file RaFAH_v0.1.pl and edit the following lines to point to the location of the previously downloaded files in your machine.
Note: edit only the text between double quotes and nothing else.

Line 37: Full path to HP_Ranger_Model_3_Valid_Cols.txt
Line 38: Full path to HP_Ranger_Model_3_Filtered_0.9_Valids.hmm
Line 39: Full path to Predict_Host_RF.R
Line 40: Full path to MMSeqs_Clusters_Ranger_Model_1+2+3_Clean.RData

Save the edited version of RaFAH_v0.1.pl

Running RaFAH:

For instruction on how to run RaFAH:

perl RaFAH_v0.1.pl --help
Source: RaFAH_README.txt, updated 2020-09-08