142 lines
4.8 KiB
Bash
142 lines
4.8 KiB
Bash
|
#!/bin/bash
|
||
|
|
#
|
||
|
|
# BUILD RRNA models
|
||
|
|
#
|
||
|
|
#========================================================================================
|
||
|
|
|
||
|
|
# -- CAUTION -- Works as long than the script
|
||
|
|
# is not called through a symlink
|
||
|
|
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
|
||
|
|
source "${THIS_DIR}/../../../scripts/bash_init.sh"
|
||
|
|
|
||
|
|
function fasta1li {
|
||
|
|
|
||
|
|
$AwkCmd '/^>/ {if (sequence) \
|
||
|
|
{print sequence}; \
|
||
|
|
print $0; \
|
||
|
|
sequence=""} \
|
||
|
|
!/^>/ {sequence = sequence $0} \
|
||
|
|
END {print sequence}' $1
|
||
|
|
}
|
||
|
|
|
||
|
|
function dereplicate {
|
||
|
|
DATA=$1
|
||
|
|
sumaclust -t 1 $DATA | \
|
||
|
|
fasta1li | \
|
||
|
|
grep -A 1 '^>' | \
|
||
|
|
grep -A1 'cluster_center=True;' | \
|
||
|
|
grep -v -- -- | \
|
||
|
|
sed -E "s/count=[0-9]+; //" | \
|
||
|
|
sed 's/cluster_weight/count/' | \
|
||
|
|
$AwkCmd ' /^>/ {SEQ++;\
|
||
|
|
match($0,"count=[0-9][0-9]*;");\
|
||
|
|
count=substr($0,RSTART,RLENGTH);\
|
||
|
|
$1=$1"_"SEQ;\
|
||
|
|
print $1,count} \
|
||
|
|
!/^>/ {print $0}'
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
function clustering {
|
||
|
|
DATA=$1
|
||
|
|
rm -rf $DATA
|
||
|
|
mkdir $DATA
|
||
|
|
sumaclust -t 0.9 $DATA.fasta | \
|
||
|
|
fasta1li > $DATA.clust.fasta
|
||
|
|
cluster=$(grep '^>' $DATA.clust.fasta | \
|
||
|
|
sed -E 's/.*cluster=([^;]+);.*$/\1/' | \
|
||
|
|
sort -u)
|
||
|
|
for c in $cluster; do
|
||
|
|
w=$(grep "$c" "${DATA}.clust.fasta" | \
|
||
|
|
head -1 | \
|
||
|
|
sed -E 's/.*cluster_weight=([^;]+);.*$/\1/')
|
||
|
|
out=$(printf "${DATA}/%05d_%s" $w $c)
|
||
|
|
grep -A1 "$c" "${DATA}.clust.fasta" | \
|
||
|
|
grep -v -- -- > "$out.fasta"
|
||
|
|
muscle -in "$out.fasta" -out "$out.align.fasta"
|
||
|
|
done
|
||
|
|
}
|
||
|
|
|
||
|
|
function revcomp {
|
||
|
|
$AwkCmd 'function printfasta(seq) { \
|
||
|
|
seqlen=length(seq); \
|
||
|
|
for (i=1; i <= seqlen; i+=60) \
|
||
|
|
print substr(seq,i,60); \
|
||
|
|
} \
|
||
|
|
function comp(seq) { \
|
||
|
|
"echo "seq" | tr acgtACGT tgcaTGCA " | getline res; \
|
||
|
|
close("echo "seq" | tr acgtACGT tgcaTGCA "); \
|
||
|
|
return res; \
|
||
|
|
} \
|
||
|
|
function rev(seq) { \
|
||
|
|
"echo "seq" | rev " | getline res; \
|
||
|
|
close("echo "seq" | rev "); \
|
||
|
|
return res; \
|
||
|
|
} \
|
||
|
|
function revcomp(seq) { \
|
||
|
|
res=rev(comp(seq)); \
|
||
|
|
return res; \
|
||
|
|
} \
|
||
|
|
\
|
||
|
|
(seq) && /^>/ {print head; \
|
||
|
|
printfasta(revcomp(seq)); \
|
||
|
|
seq=""} \
|
||
|
|
/^>/ {head=$0} \
|
||
|
|
! /^>/ {seq=seq$0} \
|
||
|
|
END { print head; \
|
||
|
|
printfasta(revcomp(seq)); \
|
||
|
|
}' $1
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
pushTmpDir ORG.buildRRNAMito
|
||
|
|
loginfo "Tempdir: $(pwd)"
|
||
|
|
|
||
|
|
openLogFile "${RRNA_DATA_DIR}/rRNA_mito_models.log"
|
||
|
|
|
||
|
|
loginfo "Selecting Metazoa genebank entries..."
|
||
|
|
METAZOA=$(${PROG_DIR}/../../normalize/tools/selectMetazoa.sh $*)
|
||
|
|
loginfo " --> $(echo ${METAZOA} | wc -w) entries selected"
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
loginfo "Extracting 12S rRNA sequences..."
|
||
|
|
rm -f raw_12S.fasta
|
||
|
|
for f in ${METAZOA}; do
|
||
|
|
loginfo "Extracting 12S rRNA sequences from ${f}..."
|
||
|
|
${PROG_DIR}/extract_ref12S.sh ${f} >> raw_12S.fasta
|
||
|
|
done
|
||
|
|
loginfo " --> $(fastaCount raw_12S.fasta) retreived sequences"
|
||
|
|
dereplicate raw_12S.fasta >> 12S.fasta
|
||
|
|
loginfo " --> $(fastaCount 12S.fasta) distinct sequences"
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
loginfo "Clustering 12S rRNA sequences..."
|
||
|
|
clustering 12S
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
loginfo "Installing 12S rRNA sequences..."
|
||
|
|
cp -r 12S "${RRNA_DATA_DIR}/RRNA_12S_mito"
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
|
||
|
|
loginfo "Extracting 16S rRNA sequences..."
|
||
|
|
rm -f raw_16S.fasta
|
||
|
|
for f in ${METAZOA}; do
|
||
|
|
${PROG_DIR}/extract_ref16S.sh ${f} >> raw_16S.fasta
|
||
|
|
done
|
||
|
|
loginfo " --> $(fastaCount raw_16S.fasta) retreived sequences"
|
||
|
|
dereplicate raw_16S.fasta > 16S.fasta
|
||
|
|
loginfo " --> $(fastaCount 16S.fasta) distinct sequences"
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
loginfo "Clustering 16S rRNA sequences..."
|
||
|
|
clustering 16S
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
loginfo "Installing 16S rRNA sequences..."
|
||
|
|
cp -r 16S "${RRNA_DATA_DIR}/RRNA_16S_mito"
|
||
|
|
loginfo "Done"
|
||
|
|
|
||
|
|
|
||
|
|
popTmpDir
|