Adds the detection of the RPS12 gene (Gene with trans-splicing)
Former-commit-id: 2396df183a925fbc1a8b398ee8dd4e12ca3c255f Former-commit-id: 309796fcdac8cf4b6379eae6418dcf1d6db21bb3
This commit is contained in:
401
detectors/cds/bin/do_rps12.sh
Executable file
401
detectors/cds/bin/do_rps12.sh
Executable file
@ -0,0 +1,401 @@
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#!/bin/bash
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#
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# Annotate the RPS12 gene of a plastide genome
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#
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#========================================================================================
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#
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# The RPS12 gene is one of the CDS coding for a riboosomal protein
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# Depending on the species, the gene is constituted of oone to three exons.
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# The exon one is not located close to the others and a trans-splicing is needed
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# to reconstruct the spliced mRNA. The exons 2 and eventuually 3 can be located in the
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# inverted repeats (IRs) and therfore they can exist in two copies. This can lead to two
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# ways to annotate RPS12
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#
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#
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# go_rps12.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the normalized genome to annotate
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#
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# Results are printed to the standart output
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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DBROOT="$CDS_DATA_DIR/chlorodb/RPS12"
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RPS12DB="${DBROOT}/RPS12_DB.clean.fst"
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DELTA=50
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SEQLEN=$(seqlength "${QUERY}")
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SEQUENCE=$(readfirstfastaseq "${QUERY}")
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pushTmpDir ORG.RPS12
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# localize the gene on the chloroplast genome using blast
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loginfo "Locating RPS12 gene by similarity..."
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blastx \
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-query ${QUERY} \
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-db ${RPS12DB} \
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-query_gencode 11 \
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-outfmt 7 \
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| $AwkCmd ' # Blast HSPs are filtered to keep only
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# at maximum the 20 first ones having an
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# e-value below 1e-20
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BEGIN {BEST_EVAL = 1e-40;
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OUT = 0}
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/^#/ {next}
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($2 == PREV_CDS) { HSPs = HSPs "\n" $0;}
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(OUT < 20) && ($2 != PREV_CDS) && (BEST_EVAL < (1e-20 + 0.0)) {
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if (PREV_CDS) print HSPs;
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HSPs = $0;
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BEST_EVAL = 1;
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PREV_CDS = $2;
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OUT++
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}
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{PREV_CDS = $2;}
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(BEST_EVAL > ($11 + 0.0)) {BEST_EVAL = ($11 + 0.0)}
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' > "rps12_locate.hsps"
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#
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# Extracting protein ids from selected blast HSPs
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#
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$AwkCmd '{print $2}' "rps12_locate.hsps" \
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| sort \
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| uniq > "dbsel.txt"
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#
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# Extract corresponding protein sequences
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# from the RPS12 database.
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#
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mkdir -p RPS12
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$AwkCmd -v FILE="dbsel.txt" \
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-f $LIB_DIR/subdb.awk ${RPS12DB} \
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> "RPS12/rps12.fasta"
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cat "rps12_locate.hsps" \
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| $AwkCmd '# Normalizes the writing of the forward and reverse strand matches
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($7 <= $8) {print $7,$8,$9,$10,"F"}
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($7 > $8) {print $8,$7,$9,$10,"R"}' \
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| sort -un \
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| $AwkCmd 'function overlap(x1,y1,x2,y2) {
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return (((x1 <= x2) && (x2 <= (y1+1))) ||
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((x2 <= x1) && (x1 <= (y2+1))))
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}
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function min(a,b) {return (a <= b) ? a:b }
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function max(a,b) {return (a >= b) ? a:b }
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(NR==1) {i=0
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frg[i]=$0
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}
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(x1 && y1) {
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if (overlap(x1,y1,$1,$2)) {
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$1 = min(x1,$1)
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$2 = max(y1,$2)
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if (overlap(v1,w1,$3,$4)) {
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$3 = min(v1,$3)
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$4 = max(w1,$4)
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}
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}
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else i++
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}
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(x1 && y1) {
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frg[i] = $0
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}
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{ x1 = $1
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y1 = $2
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v1 = $3
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w1 = $4
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}
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END {
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for (j = 0; j <= i; j++) {
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print frg[j]
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}
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}
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' \
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| sort -nk 3 \
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| $AwkCmd '($3 != old3 || $4 != old4) {
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i++
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old3=$3
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old4=$4
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}
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{print $0,i}
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' \
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| sort -nk 1 \
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| $AwkCmd 'function min(a,b) {return (a <= b) ? a:b }
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(old6 == 1) {
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print old
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oldprint = 1
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}
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((old6 == 2 && $6==2) ||
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full == 1) {
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print old
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full = 0
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}
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(((old6 == 2 && $6==3) ||
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(old6 == 3 && $6==2)) && full != 1) {
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$1 = old1
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$6 = min(old6,$6)
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full = 1
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}
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END {print old}
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{
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old = $0
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old1 = $1
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old6= $6
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}' \
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| $AwkCmd -v delta="$DELTA" \
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-v seqlen="$SEQLEN" \
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-v chloro="$SEQUENCE" \
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'function min(a,b) {return (a <= b) ? a:b }
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function max(a,b) {return (a >= b) ? a:b }
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function rev(s) {
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x = ""
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for (i=length(s);i!=0;i--)
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x=x substr(s,i,1)
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return x
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}
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function swapchar(s,a,b) {
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gsub(a,"@",s)
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gsub(b,a,s)
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gsub(/@/,b,s)
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return s
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}
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function revcomp(s) {
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s = swapchar(s,"A","T")
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s = swapchar(s,"C","G")
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s = swapchar(s,"M","K")
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s = swapchar(s,"R","Y")
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s = swapchar(s,"W","S")
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s = swapchar(s,"B","V")
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s = swapchar(s,"D","H")
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s = swapchar(s,"a","t")
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s = swapchar(s,"c","g")
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s = swapchar(s,"m","k")
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s = swapchar(s,"r","y")
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s = swapchar(s,"w","s")
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s = swapchar(s,"b","v")
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s = swapchar(s,"d","h")
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return rev(s)
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}
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{ from = max(1,$1 - delta)
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to = min($2 + delta,seqlen)
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sequence = substr(chloro,from,to-from+1)
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if ($5 == "R") sequence = revcomp(sequence)
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nparts[$6]+=1
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n = nparts[$6]
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parts[$6][n][1] = from
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parts[$6][n][2] = to
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parts[$6][n][3] = $3
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parts[$6][n][4] = $4
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parts[$6][n][5] = $5
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parts[$6][n][6] = $6
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parts[$6][n][7] = sequence
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}
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END {
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l = length(parts)
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if (l==1) {
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n = nparts[1]
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for (i =1; i <= n; i++) {
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print ">RPS12_" i,"parts=1; limit=" length(parts[1][i][7]) + 1 \
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"; from1=" parts[1][i][1] \
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"; to1=" parts[1][i][2] "; strand1=" parts[1][i][5] \
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";" > "rps12_fragments_" i ".fasta"
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print parts[1][i][7] \
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> "rps12_fragments_" i ".fasta"
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}
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}
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if (l==2) {
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n1 = nparts[1]
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n2 = nparts[2]
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for (i =1; i <= n1; i++)
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for (j =1; j <= n2; j++) {
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k = (i-1)*n2+j
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print ">RPS12_" k,"parts=2", \
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"limit=" (length(parts[1][i][7]) + 10 + 1) \
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"; from1=" parts[1][i][1] "; to1=" parts[1][i][2] "; strand1=" parts[1][i][5] \
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"; from2=" parts[2][j][1] "; to2=" parts[2][j][2] "; strand2=" parts[2][j][5] \
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";" > "rps12_fragments_" k ".fasta"
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print parts[1][i][7] "nnnnnnnnnn" parts[2][j][7] \
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> "rps12_fragments_" k ".fasta"
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}
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}
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}
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'
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#
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# Run exonarate on every fragment of chloroplast
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#
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# It should be one or two fragments
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#
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export PASS1_SPEEDUP=0
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cp $DBROOT/Annot.lst RPS12
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for f in rps12_fragments_*.fasta ; do
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tcsh -f ${PROG_DIR}/do_exonerate.csh \
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$f \
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"RPS12/rps12.fasta" \
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$DBROOT/../models $(pwd)
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done
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#
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# Rewrite the coordinates of the genes on the extracted
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# fragment to the chloroplaste genome coordinates
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#
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for f in *.res ; do
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header=$(head -1 ${f/.rps12.res/.fasta})
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L2=$(sed -E 's/^.*limit=([0-9]+);.*$/\1/' <<< $header)
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S1=$(sed -E 's/^.*strand1=(R|F);.*$/\1/' <<< $header)
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S2=$(sed -E 's/^.*strand2=(R|F);.*$/\1/' <<< $header)
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F1=$(sed -E 's/^.*from1=([0-9]+);.*$/\1/' <<< $header)
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F2=$(sed -E 's/^.*from2=([0-9]+);.*$/\1/' <<< $header)
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T1=$(sed -E 's/^.*to1=([0-9]+);.*$/\1/' <<< $header)
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T2=$(sed -E 's/^.*to2=([0-9]+);.*$/\1/' <<< $header)
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cat $f \
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| $AwkCmd -v S1="$S1" -v F1="$F1" -v T1="$T1" \
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-v S2="$S2" -v F2="$F2" -v T2="$T2" -v L2="$L2" \
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'
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function convert1p(p) {
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if (p+0 < L2) {
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I = 1
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if (S1=="F") {
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S = 1
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B = F1
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} else {
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S = -1
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B = T1
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}
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} else {
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I = L2
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if (S2=="F") {
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S = 1
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B = F2
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} else {
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S = -1
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B = T2
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}
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}
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return S*(p - I) + B
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}
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function convert(p1,p2) {
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p1 = convert1p(p1)
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p2 = convert1p(p2)
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if (p1 < p2)
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res = p1 ".." p2
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else
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res = "complement(" p2 ".." p1 ")"
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return res
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}
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/[0-9]+\.\.[0-9]+/ {
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s = $0
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r = $0
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while (length(s) > 0) {
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match(s,/[0-9]+\.\.[0-9]+/)
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range = substr(s,RSTART,RLENGTH)
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s = substr(s,RSTART+RLENGTH+1)
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match(range,/^[0-9]+/)
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from = substr(range,RSTART,RLENGTH)
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match(range,/[0-9]+$/)
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to = substr(range,RSTART,RLENGTH)
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sub(range,convert(from,to),r)
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}
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$0=r
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}
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{print $0}
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' \
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| $AwkCmd '
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#
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# Normalize join(complement(A),complement(B),complement(C)) locations
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# into complement(join(C,B,A))
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#
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/join\((complement\([0-9]+\.\.[0-9]+\),)+complement\([0-9]+\.\.[0-9]+\)\)/ \
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{
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sub(/join\(complement/,"complement(join",$0)
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gsub(/\),complement\(/,",",$0)
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match($0,/[0-9]+\.\.[0-9]+(,[0-9]+\.\.[0-9]+)*/)
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positions=substr($0,RSTART,RLENGTH)
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n = split(positions,exons,",")
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for (i=1; i<=n; i++) {
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if (i > 1)
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rexons = exons[i] "," rexons
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else
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rexons = exons[i]
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}
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sub(positions,rexons,$0)
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}
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{ print $0}
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' \
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| $AwkCmd '
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/^FT [^ ]/ && (length($0) > 80) {
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n = split($0,parts,",")
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j = 1
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for (i = 1; i <= n; i++) {
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if (length(line) + length(parts[i]) > 79) {
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print line ","
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line = "FT "
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j = i
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}
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if (i > j) line = line ","
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line = line parts[i]
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}
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$0 = line
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}
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{print $0}
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'
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done
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popTmpDir
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exit 0
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# NC_010654.fst
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# location=complement(join(77925..77967,78465..78700,52867..52980));
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# location=join(complement(52867..52980),109583..109818,110316..110358);
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# 52837 52980 1 48 R 1
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# 77928 77981 113 130 R 3
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# 78458 78712 39 132 R 2
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# 109571 109825 39 132 F 2
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# 110302 110355 113 130 F 3
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# /translation="MPTNPQLIRDARQQKKKKRGSRGLQRCPQRRGVCARVYNINPKK
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# --> MPTNPQLIRDARQQKKKKRGSRGLQRCPQRRGVCARVSNINPKK
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# ==> MPTNPQLIRDARQQKKKKRGSRGLQRCPQRRGVCARVSNINPKK
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# PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVKYRIVRGTL
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# --> PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVKYRIVRGTL
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# ==> PNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVKYRIVRGTL
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# DAVAVKNRQQGRSSAIWSQKAEKKVIHF"
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# --> DAVAVKNRQQGRSSAIWSQKAEKKVIHF
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# ==> DAVAVKNRQQGRSSAIWSQKAEKKVIHF
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# ADL.norm.fasta
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# 69300 69425 1 42 R 1
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# 97365 97670 36 137 R 2
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# 130601 130906 36 137 F 2
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# NC_008822
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# location=90942..91313;
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# 90942 91310 1 123 F 1
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# location=complement(join(77925..77967,78465..78700,52867..52980));
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# >RPS12_1 parts=2 limit=255; from1=52787; to1=53030; strand1=R; from2=77878; to2=78762; strand2=R;
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# join(51..159,312..553,1051..1092)
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# location=join(complement(52867..52980),109583..109818,110316..110358);
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# >RPS12_2 parts=2 limit=254; from1=52787; to1=53030; strand1=R; from2=109521; to2=110405; strand2=F;
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# join\((complement\([0-9]+\.\.[0-9]+\),)+complement\([0-9]+\.\.[0-9]+\)\)
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@ -89,6 +89,8 @@ cp $temp/genome.cds.fasta $Genome.cds.fasta
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# pass2: transsplicing
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#
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$PROG_DIR/do_rps12.sh $Fasta > $temp/$Genome.rps12.res
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#
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# pass3: prokov
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#
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