miga-base 0.5.1.0 → 0.5.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f6888c1ce3756b8cc708736c0da052e5a7396277e0c903ebcfc083f17b6915e7
-  data.tar.gz: d998f6e087316a81de4aa8897452344c1987ce0cb9807f4a1e11a29f52dfbcf2
+  metadata.gz: 5f447271e82d3343b44f79480c0133223af203dce8bb709ac7e389a559a4960f
+  data.tar.gz: fe31c84fe318692a636df5eb85f45e8cec7a1b05e399ebacbac16113e3b84a2a
 SHA512:
-  metadata.gz: c6f7f8af791664b2bb704744535e0e39c4d5fc06521beb8feb57f658d6187a667100fde4312a3a8e5f47f5dd9d4b3c06326584d95e80262dc0e02a91795e192c
-  data.tar.gz: 4f633972d8ccc1cc06cc14ca6c48b50759d63af72ba75514a0e877a58af4e1d407fda2c2608c2077dd541e30e86add8359bc2e0838d93a19f7cc1bd5c5f5fff2
+  metadata.gz: 36f741d0157aa77e60d87fb6bd8bb5038923833a9ef4d40e405cb43b50f6b4ac88b24498e22a21c12987f933bbddd553ba6e01fc7435b1e4d838e9a7b55255fd
+  data.tar.gz: c4060a6f20c403c339ca161d721ee71c4e5a268703214a614b93be3c443021c4c954bc87e72587f96a0eb40b6cfe4b6234ab0d2bb4218e4cc686dff93d2aeccd

data/lib/miga/daemon.rb

@@ -203,7 +203,7 @@ class MiGA::Daemon < MiGA::MiGA
       else
         (job[:ds].nil? ? project : job[:ds]).add_result(job[:job], false).nil?
       end
-      say "Completed pid:#{job[:pid]} for #{job[:task_name]}." unless ongoing
+      say "Completed pid:#{job[:pid]} for #{job[:task_name]}" unless ongoing
       ongoing
     end
     # Avoid single datasets hogging resources

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.5, 1, 0]
+  VERSION = [0.5, 2, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 1, 6)
+  VERSION_DATE = Date.new(2020, 1, 7)
 
   ##
   # Reference of MiGA.

data/scripts/cds.bash

@@ -17,14 +17,38 @@ if [[ -e "../05.assembly/$DATASET.LargeContigs.fna.gz" \
 fi
 
 # Run Prodigal
-TYPE=$(miga list_datasets -P "$PROJECT" -D "$DATASET" \
-   --metadata "type" | awk '{print $2}')
+TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
 case "$TYPE" in
-  metagenome|virome) PROCEDURE=meta ;;
-  *) PROCEDURE=single ;;
+  metagenome|virome)
+    $CMD -p meta
+    prodigal -a "${DATASET}.faa" -d "${DATASET}.fna" -o "${DATASET}.gff3" \
+      -f gff -q -i "../05.assembly/${DATASET}.LargeContigs.fna" -p meta
+    ;;
+  *)
+    P_LEN=0
+    BEST_CT=0
+    echo "# Codon table selection:" > "${DATASET}.ct.t"
+    for ct in 4 11 ; do
+      prodigal -a "${DATASET}.faa.$ct" -d "${DATASET}.fna.$ct" \
+        -o "${DATASET}.gff3.$ct" -f gff -q -p single -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}')
+      echo "# codon table $ct total length: $C_LEN aa" \
+        >> "${DATASET}.ct.t"
+      if [[ $C_LEN > $P_LEN ]] ; then
+        for x in faa fna gff3 ; do
+          mv "${DATASET}.$x.$ct" "${DATASET}.$x"
+        done
+        P_LEN=$C_LEN
+        BEST_CT=$ct
+      else
+        rm "$DATASET".*."$ct"
+      fi
+    done
+    echo "# Selected table: $BEST_CT"
+    ;;
 esac
-prodigal -a "$DATASET.faa" -d "$DATASET.fna" -f gff -o "$DATASET.gff3" \
-  -p $PROCEDURE -q -i "../05.assembly/$DATASET.LargeContigs.fna"
 
 # Clean Prodigal noisy deflines
 for i in faa fna ; do
@@ -34,6 +58,10 @@ done
 perl -pe 's/ID=([0-9]+_[0-9]+);/ID=gene_$1;/' "$DATASET.gff3" \
   > "$DATASET.gff3.t"
 mv "$DATASET.gff3.t" "$DATASET.gff3"
+if [[ -e "${DATASET}.ct.t" ]] ; then
+  cat "${DATASET}.ct.t" >> "${DATASET}.gff3"
+  rm "${DATASET}.ct.t"
+fi
 
 # Gzip
 for ext in gff3 faa fna ; do
@@ -43,3 +71,4 @@ done
 # Finalize
 miga date > "$DATASET.done"
 miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+

data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl

@@ -1 +1 @@
-../../Scripts/FastA.N50.pl
+utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl

@@ -1 +1 @@
-../../Scripts/FastA.filterN.pl
+utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl

@@ -1 +1 @@
-../../Scripts/FastA.length.pl
+utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl

data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl

@@ -1 +1 @@
-../../Scripts/FastA.split.pl
+utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl

data/utils/enveomics/Scripts/lib/enveomics.R

@@ -1 +1 @@
-../../enveomics.R
+utils/enveomics/Scripts/lib/../../enveomics.R

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.5.1.0
+  version: 0.5.2.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-01-06 00:00:00.000000000 Z
+date: 2020-01-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -515,7 +515,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubyforge_project: 
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: MiGA