Plasmids

DerrickWood · Feb 18, 2015 · 6a7e388 · 6a7e388
1 parent 7cb3b05
commit 6a7e388
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Showing 2 changed files with 21 additions and 3 deletions.
diff --git a/scripts/download_genomic_library.sh b/scripts/download_genomic_library.sh
@@ -20,6 +20,7 @@
 # Download specific genomic libraries for use with Kraken.
 # Supported choices are:
 #   bacteria - NCBI RefSeq complete bacterial/archaeal genomes
+#   plasmids - NCBI RefSeq plasmid sequences
 #   viruses - NCBI RefSeq complete viral DNA and RNA genomes
 #   human - NCBI RefSeq GRCh38 human reference genome
 
@@ -49,6 +50,22 @@ case "$1" in
       echo "Skipping download of bacterial genomes, already downloaded here."
     fi
     ;;
+  "plasmids")
+    mkdir -p $LIBRARY_DIR/Plasmids
+    cd $LIBRARY_DIR/Plasmids
+    if [ ! -e "lib.complete" ]
+    then
+      rm -f plasmids.all.fna.tar.gz
+      wget $FTP_SERVER/genomes/Plasmids/plasmids.all.fna.tar.gz
+      echo -n "Unpacking..."
+      tar zxf plasmids.all.fna.tar.gz
+      rm plasmids.all.fna.tar.gz
+      echo " complete."
+      touch "lib.complete"
+    else
+      echo "Skipping download of plasmids, already downloaded here."
+    fi
+    ;;
   "viruses")
     mkdir -p $LIBRARY_DIR/Viruses
     cd $LIBRARY_DIR/Viruses
@@ -97,6 +114,6 @@ case "$1" in
     ;;
   *)
     echo "Unsupported library.  Valid options are: "
-    echo "  bacteria virus human"
+    echo "  bacteria plasmids virus human"
     ;;
 esac
diff --git a/scripts/kraken-build b/scripts/kraken-build
@@ -40,7 +40,7 @@ my $DEF_MINIMIZER_LEN = 15;
 my $DEF_KMER_LEN = 31;
 my $DEF_THREAD_CT = 1;
 
-my @VALID_LIBRARY_TYPES = qw/bacteria viruses human/;
+my @VALID_LIBRARY_TYPES = qw/bacteria plasmids viruses human/;
 
 # Option/task option variables
 my (
@@ -199,7 +199,8 @@ Usage: $PROG [task option] [options]
 Task options (exactly one must be selected):
   --download-taxonomy        Download NCBI taxonomic information
   --download-library TYPE    Download partial library
-                             (TYPE = one of "bacteria", "viruses", "human")
+                             (TYPE = one of "bacteria", "plasmids", 
+                             "viruses", "human")
   --add-to-library FILE      Add FILE to library
   --build                    Create DB from library
                              (requires taxonomy d/l'ed and at least one file