Adaptive Prodigal call for short assemblies

bio-miga · Aug 29, 2024 · eed9d36 · eed9d36
1 parent 7f5fcaf
commit eed9d36
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/lib/miga/version.rb b/lib/miga/version.rb
@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 20, 1].freeze
+  VERSION = [1.3, 20, 2].freeze
 
   ##
   # Nickname for the current major.minor version.
   VERSION_NAME = 'mezzotint'
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 7, 25)
+  VERSION_DATE = Date.new(2024, 8, 29)
 
   ##
   # References of MiGA

diff --git a/scripts/cds.bash b/scripts/cds.bash
@@ -26,10 +26,14 @@ case "$TYPE" in
   *)
     P_LEN=0
     BEST_CT=0
+    PROCEDURE=single
+    ASM_LEN=$(grep -v '^>' "../05.assembly/${DATASET}.LargeContigs.fna" \
+      | wc -lc | awk '{ print $2-$1 }')
+    [[ "$ASM_LEN" -lt 2000 ]] && PROCEDURE=meta
     echo "# Codon table selection:" > "${DATASET}.ct.t"
     for ct in 11 4 ; do
       prodigal -a "${DATASET}.faa.$ct" -d "${DATASET}.fna.$ct" \
-        -o "${DATASET}.gff3.$ct" -f gff -q -p single -g "$ct" \
+        -o "${DATASET}.gff3.$ct" -f gff -q -p $PROCEDURE -g "$ct" \
         -i "../05.assembly/${DATASET}.LargeContigs.fna"
       C_LEN=$(grep -v '^>' "${DATASET}.faa.$ct" \
         | perl -pe 's/[^A-Z]//ig' | wc -c | awk '{print $1}')