Eric Coissac
06f36ccdd3
Former-commit-id: 1b155125047cbee1cccd12ee6865502f36172566 Former-commit-id: bf4174556214216eeb4e1720c5e9e3cb482bae2b
461 lines
16 KiB
Bash
Executable File
461 lines
16 KiB
Bash
Executable File
#!/bin/bash
|
|
#
|
|
# Annotate the RPS12 gene of a plastide genome
|
|
#
|
|
#========================================================================================
|
|
#
|
|
# The RPS12 gene is one of the CDS coding for a riboosomal protein
|
|
# Depending on the species, the gene is constituted of oone to three exons.
|
|
# The exon one is not located close to the others and a trans-splicing is needed
|
|
# to reconstruct the spliced mRNA. The exons 2 and eventuually 3 can be located in the
|
|
# inverted repeats (IRs) and therfore they can exist in two copies. This can lead to two
|
|
# ways to annotate RPS12
|
|
#
|
|
#
|
|
# go_rps12.sh <FASTAFILE>
|
|
#
|
|
# - <FASTAFILE> : The fasta file containing the normalized genome to annotate
|
|
#
|
|
# Results are printed to the standart output
|
|
#
|
|
#========================================================================================
|
|
|
|
# -- 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"
|
|
|
|
if [[ ! "$1" =~ ^/ ]]; then
|
|
QUERY="${CALL_DIR}/$1"
|
|
else
|
|
QUERY="$1"
|
|
fi
|
|
|
|
if (( $# > 1 )) ; then
|
|
TEMP=$2
|
|
else
|
|
TEMP=""
|
|
fi
|
|
|
|
DBROOT="$CDS_DATA_DIR/sp_chlorodb/RPS12"
|
|
RPS12DB="${DBROOT}/rps12.fst"
|
|
DELTA=50
|
|
|
|
AnnotFile="$CDS_DATA_DIR/sp_chlorodb/Annot.lst"
|
|
ModelsDir="$CDS_DATA_DIR/sp_chlorodb/models"
|
|
|
|
SEQLEN=$(seqlength "${QUERY}")
|
|
SEQUENCE=$(readfirstfastaseq "${QUERY}")
|
|
|
|
pushTmpDir ORG.RPS12
|
|
|
|
# localize the gene on the chloroplast genome using blast
|
|
loginfo "Locating RPS12 gene by similarity..."
|
|
|
|
|
|
blastx \
|
|
-query ${QUERY} \
|
|
-db ${RPS12DB} \
|
|
-query_gencode 11 \
|
|
-outfmt 7 \
|
|
| $AwkCmd ' # Blast HSPs are filtered to keep only
|
|
# at maximum the 20 first ones having an
|
|
# e-value below 1e-20
|
|
BEGIN {BEST_EVAL = 1e-40;
|
|
OUT = 0}
|
|
/^#/ {next}
|
|
($2 == PREV_CDS) && (($11 + 0.0) < (1e-5 + 0.0)) {
|
|
HSPs = HSPs "\n" $0;
|
|
}
|
|
|
|
(OUT < 20) && ($2 != PREV_CDS) && (BEST_EVAL < (1e-20 + 0.0)) {
|
|
if (PREV_CDS) print HSPs;
|
|
HSPs = $0;
|
|
BEST_EVAL = 1;
|
|
PREV_CDS = $2;
|
|
OUT++
|
|
}
|
|
{PREV_CDS = $2;}
|
|
|
|
(BEST_EVAL > ($11 + 0.0)) {BEST_EVAL = ($11 + 0.0)}
|
|
' > "rps12_locate.hsps"
|
|
|
|
|
|
#
|
|
# Extracting protein ids from selected blast HSPs
|
|
#
|
|
|
|
$AwkCmd '{print $2}' "rps12_locate.hsps" \
|
|
| sort \
|
|
| uniq > "dbsel.txt"
|
|
|
|
#
|
|
# Extract corresponding protein sequences
|
|
# from the RPS12 database.
|
|
#
|
|
|
|
mkdir -p RPS12
|
|
$AwkCmd -v FILE="dbsel.txt" \
|
|
-f $LIB_DIR/subdb.awk ${RPS12DB} \
|
|
> "RPS12/rps12.fasta"
|
|
|
|
cat "rps12_locate.hsps" \
|
|
| $AwkCmd '# Normalizes the writing of the forward and reverse strand matches
|
|
($7 <= $8) {print $7,$8,$9,$10,"F"}
|
|
($7 > $8) {print $8,$7,$9,$10,"R"}' \
|
|
| sort -n \
|
|
| uniq \
|
|
| $AwkCmd 'function overlap(x1,y1,x2,y2) {
|
|
return (((x1+0 <= x2+0) && ((y1+1) >= x2+0)) ||
|
|
((x2+0 <= x1+0) && ((y2+1) >= x1+0)))
|
|
}
|
|
function min(a,b) {return (a <= b) ? a:b }
|
|
function max(a,b) {return (a >= b) ? a:b }
|
|
(NR==1) {i=0
|
|
frg[i]=$0
|
|
}
|
|
(x1 && y1) {
|
|
if (overlap(x1,y1,$1,$2)) {
|
|
$1 = min(x1,$1)
|
|
$2 = max(y1,$2)
|
|
if (overlap(v1,w1,$3,$4)) {
|
|
$3 = min(v1,$3)
|
|
$4 = max(w1,$4)
|
|
}
|
|
}
|
|
else i++
|
|
}
|
|
(x1 && y1) {
|
|
frg[i] = $0
|
|
}
|
|
{ x1 = $1
|
|
y1 = $2
|
|
v1 = $3
|
|
w1 = $4
|
|
}
|
|
END {
|
|
for (j = 0; j <= i; j++) {
|
|
print frg[j]
|
|
}
|
|
}
|
|
' \
|
|
| sort -nk 3 \
|
|
| $AwkCmd '($3 != old3 || $4 != old4) {
|
|
i++
|
|
old3=$3
|
|
old4=$4
|
|
}
|
|
{print $0,i}
|
|
' \
|
|
| sort -nk 6 \
|
|
| $AwkCmd 'function min(a,b) {return (a <= b) ? a:b }
|
|
(old6 == 1) {
|
|
print old
|
|
oldprint = 1
|
|
}
|
|
((old6 == 2 && $6==2) ||
|
|
full == 1) {
|
|
print old
|
|
full = 0
|
|
}
|
|
(((old6 == 2 && $6==3) ||
|
|
(old6 == 3 && $6==2)) && full != 1) {
|
|
$1 = old1
|
|
$6 = min(old6,$6)
|
|
full = 1
|
|
}
|
|
END {print old}
|
|
{
|
|
old = $0
|
|
old1 = $1
|
|
old6= $6
|
|
}' \
|
|
| $AwkCmd -v delta="$DELTA" \
|
|
-v seqlen="$SEQLEN" \
|
|
-v chloro="$SEQUENCE" \
|
|
'function min(a,b) {return (a <= b) ? a:b }
|
|
function max(a,b) {return (a >= b) ? a:b }
|
|
function rev(s) {
|
|
x = ""
|
|
for (i=length(s);i!=0;i--)
|
|
x=x substr(s,i,1)
|
|
return x
|
|
}
|
|
function swapchar(s,a,b) {
|
|
gsub(a,"@",s)
|
|
gsub(b,a,s)
|
|
gsub(/@/,b,s)
|
|
return s
|
|
}
|
|
function revcomp(s) {
|
|
s = swapchar(s,"A","T")
|
|
s = swapchar(s,"C","G")
|
|
s = swapchar(s,"M","K")
|
|
s = swapchar(s,"R","Y")
|
|
s = swapchar(s,"W","S")
|
|
s = swapchar(s,"B","V")
|
|
s = swapchar(s,"D","H")
|
|
s = swapchar(s,"a","t")
|
|
s = swapchar(s,"c","g")
|
|
s = swapchar(s,"m","k")
|
|
s = swapchar(s,"r","y")
|
|
s = swapchar(s,"w","s")
|
|
s = swapchar(s,"b","v")
|
|
s = swapchar(s,"d","h")
|
|
return rev(s)
|
|
}
|
|
{ from = max(1,$1 - delta)
|
|
to = min($2 + delta,seqlen)
|
|
sequence = substr(chloro,from,to-from+1)
|
|
if ($5 == "R") sequence = revcomp(sequence)
|
|
nparts[$6]+=1
|
|
n = nparts[$6]
|
|
parts[$6][n][1] = from
|
|
parts[$6][n][2] = to
|
|
parts[$6][n][3] = $3
|
|
parts[$6][n][4] = $4
|
|
parts[$6][n][5] = $5
|
|
parts[$6][n][6] = $6
|
|
parts[$6][n][7] = sequence
|
|
}
|
|
END {
|
|
l = length(parts)
|
|
if (l==1) {
|
|
n = nparts[1]
|
|
for (i =1; i <= n; i++) {
|
|
print ">RPS12_" i,"parts=1; limit=" length(parts[1][i][7]) + 1 \
|
|
"; from1=" parts[1][i][1] \
|
|
"; to1=" parts[1][i][2] "; strand1=" parts[1][i][5] \
|
|
";" > "rps12_fragments_" i ".fasta"
|
|
print parts[1][i][7] \
|
|
> "rps12_fragments_" i ".fasta"
|
|
}
|
|
}
|
|
|
|
if (l==2) {
|
|
n1 = nparts[1]
|
|
n2 = nparts[2]
|
|
for (i =1; i <= n1; i++)
|
|
for (j =1; j <= n2; j++) {
|
|
k = (i-1)*n2+j
|
|
print ">RPS12_" k,"parts=2", \
|
|
"limit=" (length(parts[1][i][7]) + 10 + 1) \
|
|
"; from1=" parts[1][i][1] "; to1=" parts[1][i][2] "; strand1=" parts[1][i][5] \
|
|
"; from2=" parts[2][j][1] "; to2=" parts[2][j][2] "; strand2=" parts[2][j][5] \
|
|
";" > "rps12_fragments_" k ".fasta"
|
|
print parts[1][i][7] "nnnnnnnnnn" parts[2][j][7] \
|
|
> "rps12_fragments_" k ".fasta"
|
|
|
|
}
|
|
}
|
|
}
|
|
'
|
|
|
|
nrps12=$(ls -1 rps12_fragments_*.fasta | wc -l)
|
|
|
|
if (( nrps12 > 1 )) ; then
|
|
message="$nrps12 versions"
|
|
else
|
|
message="$nrps12 version"
|
|
fi
|
|
|
|
loginfo "$message of the gene rps12 detected."
|
|
|
|
#
|
|
# Run exonarate on every fragment of chloroplast
|
|
#
|
|
# It should be one or two fragments
|
|
#
|
|
export PASS1_SPEEDUP=0
|
|
nbseq=0
|
|
for fasta in rps12_fragments_*.fasta ; do
|
|
tcsh -f ${PROG_DIR}/do_exonerate.csh \
|
|
Pass2 \
|
|
$fasta \
|
|
"RPS12/rps12.fasta" \
|
|
$AnnotFile \
|
|
$ModelsDir $(pwd)
|
|
((nbseq=nbseq+1))
|
|
done
|
|
|
|
#
|
|
# Rewrite the coordinates of the genes on the extracted
|
|
# fragment to the chloroplaste genome coordinates
|
|
#
|
|
|
|
n=0
|
|
for f in *.res ; do
|
|
((n=n+1))
|
|
mv $f $f.ori
|
|
if [[ -z "$TEMP" ]] ; then
|
|
dest="/dev/stdout"
|
|
else
|
|
dest="$TEMP/$f"
|
|
fi
|
|
header=$(head -1 ${f/.rps12.res/.fasta})
|
|
L2=$(sed -E 's/^.*limit=([0-9]+);.*$/\1/' <<< $header)
|
|
S1=$(sed -E 's/^.*strand1=(R|F);.*$/\1/' <<< $header)
|
|
S2=$(sed -E 's/^.*strand2=(R|F);.*$/\1/' <<< $header)
|
|
F1=$(sed -E 's/^.*from1=([0-9]+);.*$/\1/' <<< $header)
|
|
F2=$(sed -E 's/^.*from2=([0-9]+);.*$/\1/' <<< $header)
|
|
T1=$(sed -E 's/^.*to1=([0-9]+);.*$/\1/' <<< $header)
|
|
T2=$(sed -E 's/^.*to2=([0-9]+);.*$/\1/' <<< $header)
|
|
cat $f.ori \
|
|
| $AwkCmd -v S1="$S1" -v F1="$F1" -v T1="$T1" \
|
|
-v S2="$S2" -v F2="$F2" -v T2="$T2" -v L2="$L2" \
|
|
'
|
|
function convert1p(p) {
|
|
if (p+0 < L2) {
|
|
I = 1
|
|
if (S1=="F") {
|
|
S = 1
|
|
B = F1
|
|
} else {
|
|
S = -1
|
|
B = T1
|
|
}
|
|
} else {
|
|
I = L2
|
|
if (S2=="F") {
|
|
S = 1
|
|
B = F2
|
|
} else {
|
|
S = -1
|
|
B = T2
|
|
}
|
|
}
|
|
return S*(p - I) + B
|
|
}
|
|
function convert(p1,p2) {
|
|
p1 = convert1p(p1)
|
|
p2 = convert1p(p2)
|
|
if (p1 < p2)
|
|
res = p1 ".." p2
|
|
else
|
|
res = "complement(" p2 ".." p1 ")"
|
|
return res
|
|
}
|
|
/[0-9]+\.\.[0-9]+/ {
|
|
s = $0
|
|
r = $0
|
|
while (length(s) > 0) {
|
|
match(s,/[0-9]+\.\.[0-9]+/)
|
|
range = substr(s,RSTART,RLENGTH)
|
|
s = substr(s,RSTART+RLENGTH+1)
|
|
match(range,/^[0-9]+/)
|
|
from = substr(range,RSTART,RLENGTH)
|
|
match(range,/[0-9]+$/)
|
|
to = substr(range,RSTART,RLENGTH)
|
|
sub(range,convert(from,to),r)
|
|
}
|
|
$0=r
|
|
}
|
|
{print $0}
|
|
' \
|
|
| $AwkCmd '
|
|
#
|
|
# Normalize join(complement(A),complement(B),complement(C)) locations
|
|
# into complement(join(C,B,A))
|
|
#
|
|
/join\((complement\([0-9]+\.\.[0-9]+\),)+complement\([0-9]+\.\.[0-9]+\)\)/ \
|
|
{
|
|
sub(/join\(complement/,"complement(join",$0)
|
|
gsub(/\),complement\(/,",",$0)
|
|
match($0,/[0-9]+\.\.[0-9]+(,[0-9]+\.\.[0-9]+)*/)
|
|
positions=substr($0,RSTART,RLENGTH)
|
|
n = split(positions,exons,",")
|
|
for (i=1; i<=n; i++) {
|
|
if (i > 1)
|
|
rexons = exons[i] "," rexons
|
|
else
|
|
rexons = exons[i]
|
|
}
|
|
sub(positions,rexons,$0)
|
|
}
|
|
{ print $0}
|
|
' \
|
|
| $AwkCmd '
|
|
/^FT [^ ]/ && (length($0) > 80) {
|
|
n = split($0,parts,",")
|
|
j = 1
|
|
for (i = 1; i <= n; i++) {
|
|
if (length(line) + length(parts[i]) > 78) {
|
|
print line ","
|
|
line = "FT "
|
|
j = i
|
|
}
|
|
if (i > j) line = line ","
|
|
line = line parts[i]
|
|
}
|
|
$0 = line
|
|
}
|
|
{print $0}
|
|
' | \
|
|
$AwkCmd -v n=$n -v nbseq=$nbseq '
|
|
/^FT +\/gene="rps12"/ && (nbseq > 1) {
|
|
sub(/rps12/,"rps12_" n,$0)
|
|
}
|
|
{
|
|
print $0
|
|
}
|
|
' | \
|
|
$AwkCmd '
|
|
#
|
|
# Adds the trans_splicing qualifier
|
|
#
|
|
/^FT \/translation=/ {
|
|
print "FT /trans_splicing"
|
|
}
|
|
{
|
|
print $0
|
|
}
|
|
' > $dest
|
|
done
|
|
|
|
|
|
popTmpDir
|
|
|
|
exit 0
|
|
|
|
# NC_010654.fst
|
|
# location=complement(join(77925..77967,78465..78700,52867..52980));
|
|
# location=join(complement(52867..52980),109583..109818,110316..110358);
|
|
# 52837 52980 1 48 R 1
|
|
# 77928 77981 113 130 R 3
|
|
# 78458 78712 39 132 R 2
|
|
# 109571 109825 39 132 F 2
|
|
# 110302 110355 113 130 F 3
|
|
# /translation="MPTNPQLIRDARQQKKKKRGSRGLQRCPQRRGVCARVYNINPKK
|
|
# --> MPTNPQLIRDARQQKKKKRGSRGLQRCPQRRGVCARVSNINPKK
|
|
# ==> MPTNPQLIRDARQQKKKKRGSRGLQRCPQRRGVCARVSNINPKK
|
|
# PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVKYRIVRGTL
|
|
# --> PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVKYRIVRGTL
|
|
# ==> PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVKYRIVRGTL
|
|
# DAVAVKNRQQGRSSAIWSQKAEKKVIHF"
|
|
# --> DAVAVKNRQQGRSSAIWSQKAEKKVIHF
|
|
# ==> DAVAVKNRQQGRSSAIWSQKAEKKVIHF
|
|
# ADL.norm.fasta
|
|
# 69300 69425 1 42 R 1
|
|
# 97365 97670 36 137 R 2
|
|
# 130601 130906 36 137 F 2
|
|
|
|
# NC_008822
|
|
# location=90942..91313;
|
|
# 90942 91310 1 123 F 1
|
|
|
|
# location=complement(join(77925..77967,78465..78700,52867..52980));
|
|
# >RPS12_1 parts=2 limit=255; from1=52787; to1=53030; strand1=R; from2=77878; to2=78762; strand2=R;
|
|
# join(51..159,312..553,1051..1092)
|
|
# location=join(complement(52867..52980),109583..109818,110316..110358);
|
|
# >RPS12_2 parts=2 limit=254; from1=52787; to1=53030; strand1=R; from2=109521; to2=110405; strand2=F;
|
|
# join\((complement\([0-9]+\.\.[0-9]+\),)+complement\([0-9]+\.\.[0-9]+\)\)
|
|
|
|
# cat NC_010654.annot.embl | awk -v tag="agser" 'BEGIN {n=0} /\locus_tag/ {n++; sub(/""/, sprintf("\"%s%04d\"",tag,n),$0)} {print $0}' | less
|
|
|
|
# BRR.chloro_1 NC_018117_rps12_2 96.08 102 4 0 99022 98717 36 137 9e-57 195
|
|
# BRR.chloro_1 NC_018117_rps12_2 96.08 102 4 0 141187 141492 36 137 9e-57 195
|
|
# BRR.chloro_1 NC_018117_rps12_2 94.87 39 2 0 70611 70495 1 39 2e-16 78.6
|
|
|
|
|
|
# /trans_splicing
|