Commit a72f30f9 by alain viari

CDS detector added

parent 93fac7a7
......@@ -10,22 +10,27 @@
#
# First check if binaries have been already compiled for your port
#
# $ scripts/check_port
# $ scripts/check_port.sh
#
# if it prints :
#
# + port <PORTNAME> is correctly installed
# + checking port compilation OK
#
# then everything is fine
#
# if it prints :
#
# ! port <PORTNAME> not installed
# ! Please read README.txt for proper installation
# + port not yet compiled
#
# then, you should first compile binaries for your port
# please consult: src/README.txt for details
#
# if it prints smthing like
# * XXX version A.B.C (should be >= X.Y.Z)
# * please consider installing XXX from src/_unix_tools_
#
# then, you should first compile some unix tools binaries for your port
# please consult: src/README.txt for details
#
# -------------------------
# -2- Distribution organisation
......
......@@ -19,8 +19,8 @@
# -- CAUTION -- Works as long than the script
# is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${SCRIPT_DIR}/../../normalize/lib/lookforIR.lib.sh
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${THIS_DIR}/../../normalize/lib/lookforIR.lib.sh
pushTmpDir ORG.ir
......
......@@ -24,8 +24,8 @@
# -- CAUTION -- Works as long than the script
# is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${THIS_DIR}/../lib/lookforIR.lib.sh
ORG_DEBUG=1
......
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
source "${THIS_DIR}/../../../scripts/bash_init.sh"
SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
......
......@@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than 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.buildSCDB
......
......@@ -23,8 +23,8 @@
# -- CAUTION -- Works as long than 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.coorienteSC
......
......@@ -16,8 +16,8 @@
# -- CAUTION -- Works as long than 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.rrna
......
......@@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than 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"
function fasta1li {
......
......@@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than 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"
function revcomp {
......
......@@ -5,7 +5,7 @@
#========================================================================================
#
# Annotate tRNA based on the Aragorn software predictions.
#
# go_trna.sh <FASTAFILE>
#
# - <FASTAFILE> : The fasta file containing the genome to annotate
......@@ -14,10 +14,10 @@
#
#========================================================================================
# -- 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.trna
......
......@@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than 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"
function fasta1li {
......
......@@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than 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"
function taxid {
egrep '/db_xref="taxon:[0-9]+"' $1 | \
......
#!/bin/bash
#
#
#
# Annotate tRNA
# Annotate Organelle
#
#========================================================================================
#
# Annotate tRNA based on the Aragorn software predictions.
# go_trna.sh <FASTAFILE>
#
# - <FASTAFILE> : The fasta file containing the genome to annotate
#
# Results are printed to the standart output
#
#========================================================================================
# -- CAUTION -- Works as long than the script
# -- CAUTION -- Works as long as the script
# is not called through a symlink
SCRIPT_DIR="$(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"
......
......@@ -143,27 +143,35 @@ function formatfasta {
#
#
# The absolute path to the ORG.Annote home direcotory
# The absolute path to the ORG.Annot home directory
ORG_HOME=`getAbsolutePath $(dirname ${BASH_SOURCE[0]})/..`
ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annnote instance
ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annot instance
BIN_DIR="${ORG_HOME}/ports/${ORG_PORTNAME}/bin" # Directory containing binaries for this port
SCRIPT_DIR="${ORG_HOME}/scripts" # Directory containing scripts utilities
PROG_DIR="$(getAbsolutePath $(dirname $0))" # Directory containing the main script file
DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
LIB_DIR="$(getAbsolutePath ${PROG_DIR}/../lib)" # Directory containing the main script libraries
CALL_DIR="$(getAbsolutePath $(pwd))" # Directory from where the main script is called
IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to the
# Inverted repeat strucuture
TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to the
# tRNA detection
DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to
# IRs detection
TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
# tRNAs detection
CDS_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
# CDSs detection
RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
# rRNA dectection
RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to
# rRNAs detection
#
......@@ -179,11 +187,10 @@ RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
#
# We alter the path to include the bin dir corresponding to the port
PATH="${ORG_HOME}/ports/${ORG_PORTNAME}/bin:${PATH}"
PATH="${SCRIPT_DIR}:${BIN_DIR}:${PATH}"
export PATH
# Force to basic international setting for a correction behaviour of AWK on mac with float
export LANG=C
export LC_ALL=C
#!/bin/csh
#
# check if port is installed
#
set ORG_HOME = `dirname $0`/..
set PORTNAME = `$ORG_HOME/config/guess_port`
if (-f $ORG_HOME/ports/$PORTNAME/bin/exonerate) then
echo "+ port $PORTNAME is correctly installed"
exit 0
endif
echo "! port $PORTNAME not installed"
echo "! Please read README.txt for proper installation"
exit 1
......@@ -14,6 +14,7 @@
# gnu tar : version >= 1.15
# gnu make : version >= 3.81
# gcc and g++ : version >= 3.4.6
# gawk : version >= 4.0.1
#
# note: valid versions of gnu tar and make are in _unix_tools_
#
......
......@@ -58,7 +58,7 @@ all: repseek install
repseek: $(OBJ) main_repseek.c
$(CC) $(CFLAGS) -o $@ $(OBJ) main_repseek.c $(LDFLAGS);
$(CC) $(CFLAGS) -o $@ $(OBJ) main_repseek.c $(LDFLAGS) $(LDLIBS);
install: repseek
......
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