Patch RPS12 detection
This commit is contained in:
Eric Coissac
@ -33,7 +33,7 @@ fi
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shift
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GENOME_LENGHT="$2"
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GENOME_LENGTH="$1"
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if (( $# > 1 )) ; then
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TEMP=$2
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@ -54,7 +54,7 @@ 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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loginfo " Considered genome length : $GENOME_LENGTH"
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blastx \
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-query ${QUERY} \
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@ -82,11 +82,126 @@ blastx \
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(BEST_EVAL > ($11 + 0.0)) {BEST_EVAL = ($11 + 0.0)}
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' \
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| $AwkCmd -v glength=${GENOME_LENGHT} \
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'!($7 + 0 > glength + 0 && $8 + 0 > glength + 0)' \
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| $AwkCmd -v glength="${GENOME_LENGTH}" \
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'!(($7 + 0) > (glength + 0) && $8 + (0 > glength + 0))' \
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| $AwkCmd ' BEGIN { FS = OFS = "\t" }
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{
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subject = $2
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bitscore = $12 + 0
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s_start = $9 + 0
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s_end = $10 + 0
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# Ajuster l ordre des coordonnées
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actual_start = (s_start < s_end) ? s_start : s_end
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actual_end = (s_start < s_end) ? s_end : s_start
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# Stocker les données
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count[subject]++
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idx = count[subject]
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starts[subject, idx] = actual_start
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ends[subject, idx] = actual_end
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scores[subject, idx] = bitscore
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lines[subject, idx] = $0
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}
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END {
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for (subject in count) {
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n = count[subject]
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# Tri par score (décroissant) puis position (croissante)
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for (i = 1; i <= n; i++) {
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for (j = i + 1; j <= n; j++) {
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if (scores[subject, i] < scores[subject, j] ||
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(scores[subject, i] == scores[subject, j] &&
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starts[subject, i] > starts[subject, j])) {
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swap(starts, subject, i, j)
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swap(ends, subject, i, j)
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swap(scores, subject, i, j)
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swap(lines, subject, i, j)
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}
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}
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}
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# Sélection des HSPs optimaux
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selected_count = 0
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delete selected_starts
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delete selected_ends
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delete selected_scores
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delete selected_lines
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for (i = 1; i <= n; i++) {
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current_start = starts[subject, i]
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current_end = ends[subject, i]
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current_score = scores[subject, i]
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current_line = lines[subject, i]
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# Vérifier les chevauchements avec les HSPs sélectionnés
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overlap_max = 0
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overlap_indices = ""
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for (j = 1; j <= selected_count; j++) {
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os = (current_start > selected_starts[j]) ? current_start : selected_starts[j]
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oe = (current_end < selected_ends[j]) ? current_end : selected_ends[j]
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if (os <= oe && (oe - os + 1) >= 15) {
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if (selected_scores[j] > overlap_max) overlap_max = selected_scores[j]
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overlap_indices = overlap_indices j " "
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}
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}
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# Appliquer les règles de sélection
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if (overlap_indices == "") {
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# Aucun chevauchement : sélectionner
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add_to_selected(current_start, current_end, current_score, current_line)
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}
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else if (current_score >= overlap_max) {
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# Supprimer les HSPs moins bons et conserver les ex æquo
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new_selected_count = 0
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delete temp_selected
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# Garder les non-chevauchants et les ex æquo
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for (j = 1; j <= selected_count; j++) {
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if (!index(overlap_indices, j " ") || selected_scores[j] == current_score) {
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temp_selected[++new_selected_count] = j
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}
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}
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# Mettre à jour la liste sélectionnée
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selected_count = 0
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for (j = 1; j <= new_selected_count; j++) {
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idx = temp_selected[j]
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selected_count++
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selected_starts[selected_count] = selected_starts[idx]
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selected_ends[selected_count] = selected_ends[idx]
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selected_scores[selected_count] = selected_scores[idx]
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selected_lines[selected_count] = selected_lines[idx]
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}
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add_to_selected(current_start, current_end, current_score, current_line)
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}
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}
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# Affichage des résultats
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for (j = 1; j <= selected_count; j++) {
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print selected_lines[j]
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}
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}
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}
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function add_to_selected(start, end, score, line) {
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selected_count++
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selected_starts[selected_count] = start
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selected_ends[selected_count] = end
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selected_scores[selected_count] = score
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selected_lines[selected_count] = line
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}
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function swap(arr, subject, i, j, tmp) {
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tmp = arr[subject, i]
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arr[subject, i] = arr[subject, j]
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arr[subject, j] = tmp
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}
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' \
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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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@ -127,6 +242,7 @@ blastx \
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-v chloro="${QUERY}" \
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-f $LIB_DIR/rps12_filter_3.awk
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nrps12=$(ls -1 rps12_fragments_*.fasta | wc -l)
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if (( nrps12 > 1 )) ; then
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@ -161,6 +277,10 @@ blastx \
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n=0
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for f in *.res ; do
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loginfo "processing $f"
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xxx=$(cat $f)
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echo -e "\n==============\n$xxx\n==============\n" 1>&2
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((n=n+1))
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mv $f $f.ori
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if [[ -z "$TEMP" ]] ; then
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@ -168,7 +288,9 @@ blastx \
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else
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dest="$TEMP/$f"
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fi
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loginfo "Destination file $dest"
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header=$(head -1 ${f/.rps12.res/.fasta})
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loginfo "Header: $header"
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L2=$(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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@ -179,7 +301,7 @@ blastx \
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cat $f.ori \
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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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-f $LIB_DIR/rps12_filter_4.awk \
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-f $LIB_DIR/rps12_filter_4.awk \
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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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@ -201,7 +323,7 @@ blastx \
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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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' \
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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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@ -237,10 +359,9 @@ blastx \
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{
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print $0
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}
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' > $dest
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done
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' > "$dest"
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done
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popTmpDir
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exit 0
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@ -37,6 +37,8 @@ needfile "$Fasta"
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GenomeLength=$1; shift
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loginfo "Genome length set to : $GenomeLength bp"
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# Genome names is set from the base
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# name of the genome file without its extension
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Genome=$(basename ${Fasta%.*})
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@ -95,7 +97,7 @@ fi
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if [[ "$cdsdetection_pass2" == "yes" ]] ; then
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loginfo "running pass2:rps12 exonerate of $Genome on $DbRoot"
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$PROG_DIR/do_rps12.sh $Fasta $GenomeLength $temp
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"$PROG_DIR/do_rps12.sh" "$Fasta" "$GenomeLength" $temp
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fi
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#
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@ -109,7 +111,7 @@ if [[ "$cdsdetection_pass3" == "yes" ]] ; then
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loginfo $fams
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loginfo "running pass3:$dir exonerate of $Genome on $DbRoot"
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for f in $fams ; do
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echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
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tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
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done
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fi
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done) | parallel -j $Threads
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@ -507,9 +507,9 @@ pushTmpDir ORG.organnot
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if [[ ! -z "${sequence}" ]] ; then
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echo "${sequence}" > toannotate.fasta
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sl=$(seqlength "toannotate.fasta")
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if (( sl >= minlength )) ; then
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loginfo "Annotated genome length: $sl bp"
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seqid=$($AwkCmd '(NR==1) {print substr($1,2,1000)}' toannotate.fasta)
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# seqid=$(tr "." "_" <<< ${seqid})
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