Merge branch 'devel'

scripts/msi

@@ -19,7 +19,7 @@
 #
 # =========================================================
 
-MSI_VERSION="0.3.5"
+MSI_VERSION="0.3.6"
 PATH2SCRIPT=$(dirname "${BASH_SOURCE[0]}" )
 ## load shell functions
 source $PATH2SCRIPT/msi_shared.sh
@@ -49,7 +49,7 @@ CD_HIT_CLUSTER_THRESHOLD=0.99
 CONF_FILE=
 GEN_FASTQC_REPORT="N"
 SKIP_BLAST="N"
-IGNORE_UNCLASSIFIED=0 ;## process (1) or not (0) the file with unclassified reads (no barcodes)
+IGNORE_UNCLASSIFIED=1 ;## process (1) or not (0) the file with unclassified reads (no barcodes)
 ## minimum number of reads that a cluster must have to pass the classification step (blastnig)
 CLUSTER_MIN_READS=1
 

scripts/msi_install.sh

@@ -324,11 +324,12 @@ function install_all {
 }
 
 function msi_to_docker {
- MSI_VERSION="0.3.5"
+ MSI_VERSION="0.3.6"
  set -e
  echo "Generating docker image with MSI...this may take a while"
  pushd $PATH2SCRIPT/..
- docker build -f msi.dockerfile -t "msi/$MSI_VERSION" .
+ #docker build -f msi.dockerfile -t "msi/$MSI_VERSION" .
+ docker build -f Dockerfile -t "msi/$MSI_VERSION" . 
  exit 0
 }
 

scripts/msi_shared.sh

@@ -144,6 +144,10 @@ function load_metadata {
  perror "file $1 not found or not readable"
  exit 1
  fi
+ if [ "$1-" == "unclassified.fastq.gz-" ]; then
+ # nothing to do
+ return
+ fi 
  MD_FILE=$1
  # experiment_id
  local FILE=$2
@@ -163,7 +167,9 @@ function load_metadata {
  set -e
  if [ "$x-" == "-" ]; then
  FILE=$(basename -s .fastq.gz $FILE )
+ set +e
  x=$(grep -i -E "$EXPERIMENT_ID" $MD_FILE| grep -i -E "(^|\s)$FILE(\s|$)" |cut -f $i)
+ set -e
  fi
  MD[$C_UP]="$x"
  export MDP_$C_UP=$i

tests/run_tests.sh

@@ -103,11 +103,45 @@ mbk_mt2w=
 mbk_sp_discard_num=
 EOF
 
+cat <<EOF > $TMPDIR/msi2.params
+METADATAFILE=tests/metadata/metadata2.tsv
+blast_refdb=$TMPDIR/refdb/db1
+CLUSTER_MIN_READS=1
+CD_HIT_CLUSTER_THRESHOLD=0.99
+EXPERIMENT_ID=
+PRIMER_MAX_ERROR=0.2
+TAXONOMY_DATA_DIR=$MSI_DIR/db
+TL_DIR=tests/samples/
+IGNORE_UNCLASSIFIED=0
+OUT_FOLDER=$TMPDIR/t5a
+CLUST_MAPPED_THRESHOLD=0.825
+CLUST_ALIGNED_THRESHOLD=0.55
+blast_evalue=0.001
+blast_max_target_seqs=20
+blast_perc_identity=70
+
+mbk_Species=96
+mbk_Genus=92
+mbk_Family=92
+mbk_AboveF=92
+mbk_TopSpecies=100
+mbk_TopGenus=1
+mbk_TopFamily=1
+mbk_TopAF=1
+mbk_rm_predicted=ssciname
+mbk_sp_discard_sp=
+mbk_mt2w=
+mbk_sp_discard_num=
+EOF
+
+
 must_succeed "msi -c $TMPDIR/msi.params"
 
 must_succeed " [ $(zcat $TMPDIR/t5a/binres.tsv.gz|cut -f 1|tail -n +2|sort -u|wc -l) == 2 ]"
 must_succeed " [ $(zcat $TMPDIR/t5a/results.tsv.gz|cut -f 1|tail -n +2|sort -u|wc -l) == 2 ]"
 
+must_succeed "msi -c $TMPDIR/msi2.params -S"
+
 
 must_succeed "msi -I tests/metadata/metadata2.tsv -i tests/samples/s4/ -o $TMPDIR/t4 -b $TMPDIR/refdb/db1"