revised figures (#3)

* Move figures to a separate folders

* Add joker

* add dbaasp parsing

* remove old scripts for old figures, add new scripts

* Add source data to the figure scripts, clean-up and update wrt to manuscript

* Add logo to readme

* Remove unnecesary logos

* add benchmarking, thresholding, joker data; remove empty files, move dbaasp data to dvc

* remove comments in scripts notebooks; optimize imports; move more fasta to dvc

Co-authored-by: Tomasz Grzegorzek <tomaszgrzegorzek@outlook.com>

Author: szymczakpau

README.md

@@ -1,5 +1,9 @@
+
+<img align="right" src="static/Frog_noOutline_2.png" width="200"> 
+
 # HydrAMP: a deep generative model for antimicrobial peptide discovery
 
+
 ### Data
 
 Data is available via [DVC](https://dvc.org/) and can be obtained by running  following commands within repo root directory:

data.dvc

@@ -1,5 +1,5 @@
-outs:
-- md5: 49f768c5257295a7c498e836d031b1ec.dir
-  size: 17708470
-  nfiles: 8
-  path: data
+outs:
+- md5: 9c332227e7ff90bd67cc4c9eee36eab8.dir
+  size: 30566627
+  nfiles: 20
+  path: data

results.dvc

@@ -1,5 +1,5 @@
-outs:
-- md5: 7c3243e85401768864f7a376c801b23c.dir
-  size: 872771514
-  nfiles: 13
-  path: results
+outs:
+- md5: 9799ab4b7688afd8a64d2000d24cc7a1.dir
+  size: 872974869
+  nfiles: 16
+  path: results

scripts/dbaasp/dbaasp.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+N=8
+END=18894 # Number of peptides in DBAASP as per 02.03.2022
+DIR=../../temp_data/json
+
+mkdir -p $DIR
+
+
+for i in $(seq 1 $END); do 
+	( 
+	curl -X GET "https://dbaasp.org/peptides/$i" -H "accept: application/json">$DIR/$i.json 
+	if [[ "$?" -eq 0 ]]; then
+		exit 0
+	fi
+	) &
+    if [[ $(jobs -r -p | wc -l) -ge $N ]]; then
+        # now there are $N jobs already running, so wait here for any job
+        # to be finished so there is a place to start next one.
+        wait -n
+    fi
+done
+
+wait
+
+echo "all done"
+
+find $DIR  -size 0 -print -delete
+