Commit ba55f354 authored by Eric Coissac's avatar Eric Coissac

Add logs to print the sequence length and if the sequence is reverse

complemented
parent 213735f5
...@@ -23,7 +23,6 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh" ...@@ -23,7 +23,6 @@ source "${THIS_DIR}/../../../scripts/bash_init.sh"
pushTmpDir ORG.its pushTmpDir ORG.its
loginfo "Normalizing nuclear rDNA cistron..." loginfo "Normalizing nuclear rDNA cistron..."
RRNADB="${NUCRRNA_DATA_DIR}/plants/nuc_RRNA.hmm" RRNADB="${NUCRRNA_DATA_DIR}/plants/nuc_RRNA.hmm"
if [[ ! "$1" =~ ^/ ]]; then if [[ ! "$1" =~ ^/ ]]; then
...@@ -32,6 +31,7 @@ pushTmpDir ORG.its ...@@ -32,6 +31,7 @@ pushTmpDir ORG.its
QUERY="$1" QUERY="$1"
fi fi
loginfo "Sequence length $(seqlength ${QUERY})"
strand=( $(hmmsearch --max ${RRNADB} ${QUERY} | \ strand=( $(hmmsearch --max ${RRNADB} ${QUERY} | \
$AwkCmd '/Query: / { \ $AwkCmd '/Query: / { \
...@@ -55,7 +55,8 @@ pushTmpDir ORG.its ...@@ -55,7 +55,8 @@ pushTmpDir ORG.its
if [[ "${strand[0]}" == "Forward" ]] ; then if [[ "${strand[0]}" == "Forward" ]] ; then
cat ${QUERY} cat ${QUERY}
else else
fastarevcomp -f ${QUERY} loginfo "Revert complement rDNA cluster cistron"
fastarevcomp ${QUERY}
fi fi
else else
logerror "Cannot determine the Cistron orientation" logerror "Cannot determine the Cistron orientation"
......
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