PhyloSkims/annotate
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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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13
README.txt
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@ -10,22 +10,27 @@
# #
# First check if binaries have been already compiled for your port # First check if binaries have been already compiled for your port
# #
# $ scripts/check_port # $ scripts/check_port.sh
# #
# if it prints : # if it prints :
# #
# + port <PORTNAME> is correctly installed # + checking port compilation OK
# #
# then everything is fine # then everything is fine
# #
# if it prints : # if it prints :
# #
# ! port <PORTNAME> not installed # + port not yet compiled
# ! Please read README.txt for proper installation
# #
# then, you should first compile binaries for your port # then, you should first compile binaries for your port
# please consult: src/README.txt for details # 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 # -2- Distribution organisation

4
detectors/ir/bin/go_ir.sh
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@ -19,8 +19,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${SCRIPT_DIR}/../../normalize/lib/lookforIR.lib.sh source ${THIS_DIR}/../../normalize/lib/lookforIR.lib.sh
pushTmpDir ORG.ir pushTmpDir ORG.ir

4
detectors/normalize/bin/go_normalize.sh
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@ -24,8 +24,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh source ${THIS_DIR}/../lib/lookforIR.lib.sh
ORG_DEBUG=1 ORG_DEBUG=1

2
detectors/normalize/lib/lookforIR.lib.sh
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@ -1,4 +1,4 @@
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py" SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"

4
detectors/normalize/tools/buildSCDB.sh
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@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
pushTmpDir ORG.buildSCDB pushTmpDir ORG.buildSCDB

4
detectors/normalize/tools/coorienteSC.sh
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@ -23,8 +23,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
pushTmpDir ORG.coorienteSC pushTmpDir ORG.coorienteSC

4
detectors/rrna/bin/go_rrna.sh
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@ -16,8 +16,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
pushTmpDir ORG.rrna pushTmpDir ORG.rrna

4
detectors/rrna/tools/buildRRNAModels.sh
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@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
function fasta1li { function fasta1li {

4
detectors/rrna/tools/revcomp_alignments.sh
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@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
function revcomp { function revcomp {

8
detectors/trna/bin/go_trna.sh
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@ -5,7 +5,7 @@
#======================================================================================== #========================================================================================
# #
# Annotate tRNA based on the Aragorn software predictions. # Annotate tRNA based on the Aragorn software predictions.
#
# go_trna.sh <FASTAFILE> # go_trna.sh <FASTAFILE>
# #
# - <FASTAFILE> : The fasta file containing the genome to annotate # - <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 # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
pushTmpDir ORG.trna pushTmpDir ORG.trna

4
detectors/trna/tools/buildCAURefDB.sh
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@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
function fasta1li { function fasta1li {

4
detectors/trna/tools/extract_refCAUtRNA.sh
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@ -6,8 +6,8 @@
# -- CAUTION -- Works as long than the script # -- CAUTION -- Works as long than the script
# is not called through a symlink # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/../../../scripts/bash_init.sh" source "${THIS_DIR}/../../../scripts/bash_init.sh"
function taxid { function taxid {
egrep '/db_xref="taxon:[0-9]+"' $1 | \ egrep '/db_xref="taxon:[0-9]+"' $1 | \

19
org-annotate.sh
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@ -1,26 +1,18 @@
#!/bin/bash #!/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 # is not called through a symlink
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${SCRIPT_DIR}/scripts/bash_init.sh" source "${THIS_DIR}/scripts/bash_init.sh"
pushTmpDir ORG.organnot pushTmpDir ORG.organnot
@ -53,6 +45,9 @@ pushTmpDir ORG.organnot
${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot" ${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
loginfo "Done." loginfo "Done."
loginfo "Annotating the CDS..."
${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
loginfo "Done."
loginfo "Printing annotations header..." loginfo "Printing annotations header..."
echo "XX" echo "XX"

29
scripts/bash_init.sh
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@ -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_HOME=`getAbsolutePath $(dirname ${BASH_SOURCE[0]})/..`
ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annot instance
ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annnote instance BIN_DIR="${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 $0))" # Directory containing the main script file PROG_DIR="$(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 $(pwd))" # Directory from where the main script is called CALL_DIR="$(getAbsolutePath $(pwd))" # Directory from where the main script is called
IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to the DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
# Inverted repeat strucuture
TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to the IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to
# tRNA detection # IRs detection
RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
# rRNA dectection # tRNAs detection
CDS_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
# CDSs detection
RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to
# rRNAs detection
# #
@ -179,11 +187,10 @@ RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
# #
# We alter the path to include the bin dir corresponding to the port # 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 export PATH
# Force to basic international setting for a correction behaviour of AWK on mac with float # Force to basic international setting for a correction behaviour of AWK on mac with float
export LANG=C export LANG=C
export LC_ALL=C export LC_ALL=C

20
scripts/check_port
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@ -1,20 +0,0 @@
#!/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

1
src/README.txt
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@ -14,6 +14,7 @@
# gnu tar : version >= 1.15 # gnu tar : version >= 1.15
# gnu make : version >= 3.81 # gnu make : version >= 3.81
# gcc and g++ : version >= 3.4.6 # gcc and g++ : version >= 3.4.6
# gawk : version >= 4.0.1
# #
# note: valid versions of gnu tar and make are in _unix_tools_ # note: valid versions of gnu tar and make are in _unix_tools_
# #

2
src/repseek/repseek-2014.09/Makefile
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@ -58,7 +58,7 @@ all: repseek install
repseek: $(OBJ) main_repseek.c repseek: $(OBJ) main_repseek.c
$(CC) $(CFLAGS) -o $@ $(OBJ) main_repseek.c $(LDFLAGS); $(CC) $(CFLAGS) -o $@ $(OBJ) main_repseek.c $(LDFLAGS) $(LDLIBS);
install: repseek install: repseek