CDS detector added

README.txt

@@ -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

detectors/ir/bin/go_ir.sh

@@ -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
 

detectors/normalize/bin/go_normalize.sh

@@ -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
 

detectors/normalize/lib/lookforIR.lib.sh

-source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
+source "${THIS_DIR}/../../../scripts/bash_init.sh"
 
 SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
 

detectors/normalize/tools/buildSCDB.sh

@@ -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
 	

detectors/normalize/tools/coorienteSC.sh

@@ -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

detectors/rrna/bin/go_rrna.sh

@@ -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
 

detectors/rrna/tools/buildRRNAModels.sh

@@ -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 {
 

detectors/rrna/tools/revcomp_alignments.sh

@@ -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 {

detectors/trna/bin/go_trna.sh

@@ -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
 

detectors/trna/tools/buildCAURefDB.sh

@@ -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 {
 

detectors/trna/tools/extract_refCAUtRNA.sh

@@ -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 | \

org-annotate.sh

 #!/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"

scripts/bash_init.sh

@@ -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
 
-

scripts/check_port

-#!/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
-
-
-

src/README.txt

@@ -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_
 #

src/repseek/repseek-2014.09/Makefile

@@ -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