Commit 48e30ca5 authored by Eric Coissac's avatar Eric Coissac

Run the annotation on the normalized sequence

parent 55a83611
......@@ -38,15 +38,15 @@ pushTmpDir ORG.organnot
loginfo "Done."
loginfo "Annotating the tRNA..."
${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
${PROG_DIR}/detectors/trna/bin/go_trna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the CDS..."
${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing annotations header..."
......@@ -96,11 +96,11 @@ pushTmpDir ORG.organnot
freq["G"]" G; "\
freq["T"]" T; "\
other" other;" \
}' ${QUERY}
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Reformating sequences..."
lines=$(wc -l ${QUERY} | awk '{print $1}')
lines=$(wc -l "${RESULTS}.norm.fasta" | awk '{print $1}')
awk -v lines=$lines ' \
! /^>/ { \
seq=tolower($0); \
......@@ -115,7 +115,7 @@ pushTmpDir ORG.organnot
if (NR==lines) \
{pos-=1}; \
printf(" %6d\n",pos) \
}' ${QUERY}
}' "${RESULTS}.norm.fasta"
loginfo "Done."
loginfo "Closing sequence part..."
......
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