Commit 213735f5 by Eric Coissac

Patch a bug in the final sequence formating occuring when the input

sequence has not 60 char per line
parent af7999b0
......@@ -46,6 +46,7 @@ BEGIN {
Entry[NbEntry]["to"] = $5+0
Entry[NbEntry]["score"] = $6+0
Entry[NbEntry]["strand"] = $7
Entry[NbEntry]["stop"] = (Align !~ "\\*")
if (valid) {
for (i = $4+0 ; i <= $5+0; i++)
Cover[i] = 1
......
......@@ -93,6 +93,12 @@ do
shift
done
loginfo "Annotating mode.....: $types"
loginfo "IR detection mode...: $irdetection"
loginfo "Organism............: $organism"
loginfo "Partial mode........: $partial"
#############################
pushTmpDir ORG.organnot
......@@ -125,7 +131,7 @@ pushTmpDir ORG.organnot
chloro)
loginfo "Annotating a plant chloroplast genome..."
if [[ "$irdetection"=="yes" ]] && (( partial == 0 )) ; then
if [[ "$irdetection" == "yes" ]] && (( partial == 0 )) ; then
loginfo "Normalizing the structure of the Chloroplast sequence..."
loginfo " LSC + IRB + SSC + IRA"
......@@ -137,6 +143,7 @@ pushTmpDir ORG.organnot
loginfo "Done."
else
loginfo "No normalization of the structure of the Chloroplast sequence..."
cat toannotate.fasta > "${RESULTS}.norm.fasta"
rm -f "${RESULTS}.annot"
touch "${RESULTS}.annot"
......@@ -167,7 +174,7 @@ pushTmpDir ORG.organnot
loginfo "Annotating a plant rDNA cistron..."
loginfo "Normalizing the structure of the cistron sequence..."
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh toannotate.fasta > "${RESULTS}.norm.fasta"
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh toannotate.fasta > "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
......@@ -232,7 +239,7 @@ pushTmpDir ORG.organnot
echo "FT /organelle=\"mitochondrion\""
;;
*)
loginfo "Nuclear sequence"
loginfo "Nuclear sequence"
;;
esac
......@@ -297,6 +304,10 @@ pushTmpDir ORG.organnot
loginfo "Reformating sequences..."
lines=$(wc -l "${RESULTS}.norm.fasta" | $AwkCmd '{print $1}')
loginfo "Sequence length $(seqlength ${RESULTS}.norm.fasta)"
loginfo "lines $lines"
formatfasta "${RESULTS}.norm.fasta" | \
$AwkCmd -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
......@@ -311,7 +322,7 @@ pushTmpDir ORG.organnot
if (NR==lines) \
{pos-=1}; \
printf(" %6d\n",pos) \
}' "${RESULTS}.norm.fasta"
}'
loginfo "Done."
loginfo "Closing sequence part..."
......
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