miga-base 1.0.5.2 → 1.1.0.0

data/scripts/essential_genes.bash

@@ -36,19 +36,15 @@ HMM.essential.rb \
   > "${DATASET}.ess/log"
 
 # Index for FastAAI
-NOMULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --no-multi \
+NOMULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --no-multi \
             | wc -l | awk '{print $1}')
 if [[ "$NOMULTI" -eq "1" ]] ; then
-  if [[ "$FAA" == *.gz ]] ; then
-    gzip -cd "$FAA" > "${DATASET}.faix"
-  else
-    cp "$FAA" "${DATASET}.faix"
-  fi
-  FastAAI --qp "${DATASET}.faix" --output "${DATASET}.faix" \
-    --ext ".faix" --index --input-paths --all-vs-all --threads "$CORES"
-  rm "${DATASET}.faix"
-  rm "${DATASET}.faix.hmm"
-  rm "${DATASET}.faix.hmm.filt"
+  echo "$FAA" > "$DATASET"
+  FastAAI build_db --protein_file "$DATASET" \
+    -o "${DATASET}.faix.d" --threads "$CORES"
+  rm "$DATASET"
+  mv "${DATASET}.faix.d/database/FastAAI_database.sqlite.db" "${DATASET}.faix"
+  rm -r "${DATASET}.faix.d"
 fi
 
 # Reduce files

data/scripts/miga.bash

@@ -3,8 +3,8 @@
 ###
 # Setup environment
 set -e
-eval "$("$MIGA/bin/miga" env)"
-SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
+eval "$("$MIGA/bin/miga-env")"
+SCRIPT=${SCRIPT:-"$(basename "$0" .bash)"}
 
 ###
 # Ancillary functions

data/test/common_test.rb

@@ -78,21 +78,21 @@ class CommonTest < Test::Unit::TestCase
 
     # Check advance when missing total
     o = capture_stderr { m.advance('x', 0) }.string
-    assert_match(/\] x *\r/, o)
+    assert_match(%r{\] x *\r}, o)
 
     # Initialize advance
-    o = capture_stderr { m.advance('x', 0, 10) }.string
-    assert_match(/\] x 0\.0% \(0\/10\) *\r/, o)
+    o = capture_stderr { m.advance('x', 0, 1001) }.string
+    assert_match(%r{\] x 0\.0% \(0/1001\) *\r}, o)
 
     # Insufficient data for prediction
     sleep(1)
-    o = capture_stderr { m.advance('x', 1, 10) }.string
-    assert_match(/\] x 10\.0% \(1\/10\) *\r/, o)
+    o = capture_stderr { m.advance('x', 1, 1000) }.string
+    assert_match(%r{\] x 0\.1% \(1/1000\) *\r}, o)
 
     # Predict time
     sleep(1)
-    o = capture_stderr { m.advance('x', 2, 10) }.string
-    assert_match(/\] x 20\.0% \(2\/10\) [7-9]s left *\r/, o)
+    o = capture_stderr { m.advance('x', 2, 1000) }.string
+    assert_match(%r{\] x 0\.2% \(2/1000\) 1\d\.\dm left *\r}, o)
   end
 
   def test_num_suffix