Adding file to get the trained model for denovo identification

.gitignore

@@ -26,6 +26,9 @@ Kaiko_volume/Kaiko_stationary_files/*
 !Kaiko_volume/Kaiko_stationary_files/ExtractUniRefMembers.py
 !Kaiko_volume/config.yaml
 
+!Kaiko_denovo/model/get_data.sh
+!Kaiko_denovo/model/README.txt
+
 # pipeline outputs and inputs
 pipeline_input/*.MGF
 pipeline_intermediary/denovo_output/*.txt

Kaiko_denovo/model/README.txt

@@ -0,0 +1 @@
+Use the script above to download the model to this folder.

Kaiko_denovo/model/get_data.sh

@@ -0,0 +1,7 @@
+# Downloading Kaiko Pre-trained model
+wget ftp://massive.ucsd.edu/MSV000083150/updates/2019-01-08_mwang87_5b6489dc/other/model/checkpoint
+wget ftp://massive.ucsd.edu/MSV000083150/updates/2019-01-08_mwang87_5b6489dc/other/model/translate.ckpt-2123500.data-00000-of-00001
+wget ftp://massive.ucsd.edu/MSV000083150/updates/2019-01-08_mwang87_5b6489dc/other/model/translate.ckpt-2123500.index
+
+# Downloading knapsack
+wget ftp://massive.ucsd.edu/MSV000083150/updates/2019-01-08_mwang87_5b6489dc/other/model/knapsack.npy

README.md

@@ -24,6 +24,8 @@ Download the following files to the ```Kaiko_volume/Kaiko_stationary_files``` fo
 
 4) [Diamond search](https://github.com/bbuchfink/diamond/releases), choosing the appropriate system. If using Docker, get the Linux version.
 
+5) Denovo model: Within the ```Kaiko_denovo/model``` folder, open the ```get_data.sh``` script to download the trained model.
+
 ### Processing
 
 1) Extract the diamond file from step 4 into its own folder within ```Kaiko_volume/Kaiko_stationary_files```, eg ```Kaiko_volume/Kaiko_stationary_files/diamond```.