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Simplify CAU tRNA reference database building to keep onlyCAU tRNA

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from plastomes where the three categories of CAU tRNA (Met/Ile/fMet)
are annotated

Former-commit-id: 67dc445698e22fe8a503c6700977c79e4817d302
Former-commit-id: 6e84303543b0752a7946bdde6e5114cfe6eef8da
This commit is contained in:
Eric Coissac
2018-04-05 17:55:31 +02:00
parent c37c175fd8
commit ee634cc779
2 changed files with 86 additions and 91 deletions
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67
detectors/trna/tools/extract_refCAUtRNA.sh
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@ -10,15 +10,39 @@ THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/../../../scripts/bash_init.sh"
function taxid {
egrep '/db_xref="taxon:[0-9]+"' $1 | \
local gbk=$1
local CAT=cat
if [[ "$gbk" =~ \.gz$ ]] ; then
CAT=gzcat
fi
$CAT $gbk | \
egrep '/db_xref="taxon:[0-9]+"' | \
sed -E 's@ +/db_xref="taxon:([0-9]+)"@\1@'
}
function ac {
head -1 $1 | $AwkCmd '{print $2}'
local gbk=$1
local CAT=cat
if [[ "$gbk" =~ \.gz$ ]] ; then
CAT=gzcat
fi
$CAT $gbk | \
head -1 | $AwkCmd '{print $2}'
}
function definition {
local gbk=$1
local CAT=cat
if [[ "$gbk" =~ \.gz$ ]] ; then
CAT=gzcat
fi
$CAT $gbk | \
$AwkCmd '/^DEFINITION/ {on=1} \
(on==1) {printf("%s ",$0)} \
(/\.$/ && (on==1)) {on=0;print ""}' $1 | \
@ -27,15 +51,23 @@ function definition {
}
function gb2fasta {
local gbk=$1
local CAT=cat
if [[ "$gbk" =~ \.gz$ ]] ; then
CAT=gzcat
fi
AC=`ac $1`
TAXID=`taxid $1`
DEFINITION=`definition $1`
echo ">${AC} taxid=${TAXID}; ${DEFINITION}"
$AwkCmd '/^\/\// {on=0} \
$CAT $gbk | \
$AwkCmd '/^\/\// {on=0} \
(on==1) {print $0} \
/^ORIGIN / {on=1}' $1 | \
/^ORIGIN / {on=1}' | \
sed -E 's/^ *[0-9]+ +//' | \
sed 's/ //g'
}
@ -58,9 +90,17 @@ function findCAUtrna {
}
function trnaAnnotations {
local gbk=$1
local CAT=cat
if [[ "$gbk" =~ \.gz$ ]] ; then
CAT=gzcat
fi
$CAT $gbk | \
$AwkCmd '/^ORIGIN/ {on=0} \
(on==1) {print $0} \
/^FEATURE/ {on=1}' $1 | \
/^FEATURE/ {on=1}' | \
$AwkCmd '/^ [^ ]/ {print ""} \
{printf("%s ",$0)} \
END {print ""}' | \
@ -91,13 +131,20 @@ function annotateCAU {
}
function writeTRNA {
TAXID=`taxid $1`
AC=`ac $1`
DEFINITION=`definition $1`
local gbk=$1
local CAT=cat
if [[ "$gbk" =~ \.gz$ ]] ; then
CAT=gzcat
fi
TRNATMP="$$.trna.txt"
local TAXID=`taxid $gbk`
local AC=`ac $gbk`
local DEFINITION=`definition $gbk`
trnaAnnotations $1 > ${TRNATMP}
local TRNATMP="$$.trna.txt"
trnaAnnotations $gbk > ${TRNATMP}
ntrna=`wc -l ${TRNATMP} | $AwkCmd '{print $1}'`
if (( ntrna > 0 )); then