Add necessary version updates and update wget_refseq for the proper work

renv.lock

@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.0.3",
+    "Version": "4.1.2",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -32,7 +32,7 @@
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.2-18",
+      "Version": "1.6-5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "08588806cba69f04797dab50627428ed"
@@ -67,7 +67,7 @@
     },
     "R6": {
       "Package": "R6",
-      "Version": "2.5.0",
+      "Version": "2.5.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "b203113193e70978a696b2809525649d"
@@ -478,7 +478,7 @@
     },
     "magrittr": {
       "Package": "magrittr",
-      "Version": "2.0.1",
+      "Version": "2.0.13,
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "41287f1ac7d28a92f0a286ed507928d3"
@@ -639,7 +639,7 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "0.4.12",
+      "Version": "1.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "0879f5388fe6e4d56d7ef0b7ccb031e5"
@@ -790,6 +790,60 @@
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "2826c5d9efb0a88f657c7a679c7106db"
-    }
+    },
+    "coin": {
+      "Package": "coin",
+      "Version": "1.4-3",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "infer": {
+      "Package": "infer",
+      "Version": "1.0.6",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "rstatix": {
+      "Package": "rstatix",
+      "Version": "0.7.2",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "forcats": {
+      "Package": "forcats",
+      "Version": "1.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "gt": {
+      "Package": "gt",
+      "Version": "0.10.1",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "PRROC": {
+      "Package": "PRROC",
+      "Version": "1.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "svglite": {
+      "Package": "svglite",
+      "Version": "2.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "viridis": {
+      "Package": "viridis",
+      "Version": "0.6.5",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "webshot": {
+      "Package": "webshot",
+      "Version": "0.5.5",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    }  
   }
-}
+}

src/refseq_wget_jobs/wget_refseq.sh

@@ -38,6 +38,12 @@ echo "CD'ing into $DIR"
 
 cd $DIR
 
+TARGET_DIR="../../data/refseq/$KINGDOM"
+
+if [ ! -d "$TARGET_DIR" ]; then
+    mkdir -p "$TARGET_DIR"
+fi
+
 cd ../../data/refseq/$KINGDOM
 
 echo "Getting assembly summary"
@@ -48,8 +54,17 @@ awk -F '\t' '{if($12=="Complete Genome") print $20}' assembly_summary.txt > asse
 
 echo "Downloading genomes"
 
-for next in $(cat assembly_summary_complete_genomes_$KINGDOM.txt); do
-          wget "$next"/*genomic.fna.gz
-done
+while IFS= read -r next; do
+    wget "$next" -O "$(basename "$next")_genomic"
+    while IFS= read -r line; do
+        link=$(echo "$line" | grep -oP '(?<=href=")[^"]+')
+
+    if [[ $link == *genomic.fna.gz && $link != *from_genomic.fna.gz ]]; then
+            wget "$next/$link" 
+            gzip -d "$link"
+        fi
+    done < "$(basename "$next")_genomic"
+    rm "$(basename "$next")_genomic"
+done < assembly_summary_complete_genomes_"$KINGDOM".txt
 
 echo "Done."