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First version of the tRNA detector and of the global organnot.sh script

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Former-commit-id: f2a75cf99b24875c90c426c2afb22a75b972bf60
Former-commit-id: 65e3dfb35df06ca69bb29b690c9a40e8940ac6bf
This commit is contained in:
Eric Coissac
2015-10-11 10:39:59 -03:00
parent 6015339839
commit c32f7cdde6
9 changed files with 175 additions and 133 deletions
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2
detectors/normalize/bin/go_normalize.sh
View File

@ -27,12 +27,14 @@
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh
ORG_DEBUG=1
pushTmpDir ORG.normalize
tmpfasta1="tmp_$$_1.fasta"
tmpfasta2="tmp_$$_2.fasta"
logdebug "Running on : $QUERY"
loginfo "Computing the genome size..."
genome_length=$(seqlength $QUERY)

8
detectors/normalize/lib/lookforIR.lib.sh
View File

@ -47,7 +47,9 @@ function lookForIR {
}
SCDB="${IR_DATA_DIR}/SC_RefDB"
QUERY="${CALL_DIR}/$1"
openLogFile "${QUERY/.*/}.log"
if [[ ! "$1" =~ ^/ ]]; then
QUERY="${CALL_DIR}/$1"
else
QUERY="$1"
fi

8
detectors/normalize/tools/buildSCDB.sh
View File

@ -31,7 +31,7 @@ pushTmpDir ORG.buildSCDB
loginfo "Building LSC coorientation graph..."
${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${LOGFILE} > LSC.tgf
${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${ORG_LOGFILE} > LSC.tgf
${PROG_DIR}/cc.py LSC.tgf > LSC.cc
loginfo " --> $(awk '{print $1}' LSC.cc | uniq | wc -l) connected componants"
loginfo "Done"
@ -73,7 +73,7 @@ pushTmpDir ORG.buildSCDB
loginfo "Checking LCS homogeneity..."
${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${LOGFILE} > LSC_RefDB.tgf
${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${ORG_LOGFILE} > LSC_RefDB.tgf
${PROG_DIR}/cc.py LSC_RefDB.tgf > LSC_RefDB.cc
NCC=$(awk '{print $1}' LSC_RefDB.cc | uniq | wc -l)
if (( $NCC == 1 )); then
@ -103,7 +103,7 @@ pushTmpDir ORG.buildSCDB
loginfo "Building SSC coorientation graph..."
${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${LOGFILE} > SSC.tgf
${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${ORG_LOGFILE} > SSC.tgf
${PROG_DIR}/cc.py SSC.tgf > SSC.cc
loginfo " --> $(awk '{print $1}' SSC.cc | uniq | wc -l) connected componants"
loginfo "Done"
@ -146,7 +146,7 @@ pushTmpDir ORG.buildSCDB
loginfo "Checking SSC homogeneity..."
${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${LOGFILE} > SSC_RefDB.tgf
${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${ORG_LOGFILE} > SSC_RefDB.tgf
${PROG_DIR}/cc.py SSC_RefDB.tgf > SSC_RefDB.cc
NCC=$(awk '{print $1}' SSC_RefDB.cc | uniq | wc -l)
if (( $NCC == 1 )); then