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CDS detector added

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Former-commit-id: a72f30f90d22cc3c7ff6059e0254e47911bb5af1
Former-commit-id: db0264bdbe5136b6e6dc44e4788175a257439643
This commit is contained in:
alain viari
2015-11-08 14:28:57 +01:00
parent 8dab2d56b2
commit efb9949075
17 changed files with 62 additions and 74 deletions
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21
org-annotate.sh
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@ -1,26 +1,18 @@
#!/bin/bash
#
#
#
# Annotate tRNA
# Annotate Organelle
#
#========================================================================================
#
# Annotate tRNA based on the Aragorn software predictions.
# go_trna.sh <FASTAFILE>
#
# - <FASTAFILE> : The fasta file containing the genome to annotate
#
# Results are printed to the standart output
#
#========================================================================================
# -- CAUTION -- Works as long than the script
# -- CAUTION -- Works as long as the script
# is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/scripts/bash_init.sh"
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/scripts/bash_init.sh"
pushTmpDir ORG.organnot
@ -52,7 +44,10 @@ pushTmpDir ORG.organnot
loginfo "Annotating the rRNA genes..."
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Annotating the CDS..."
${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing annotations header..."
echo "XX"