9108ce75f1
Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1 Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984
136 lines
2.7 KiB
Awk
136 lines
2.7 KiB
Awk
#
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# extend start/stop
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#
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# -v FASTA START_MODEL STOP_MODEL START_WALK STOP_WALK
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#
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function UpStart(pos, strand, _local_, seq, i, imax, smax, s) {
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seq = Seq
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if (strand == "-") {
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pos = LenSeq - pos + 1
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seq = RevSeq
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}
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imax = 0
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smax = 0
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for (i = pos ; i >= Max(1, pos-START_WALK) ; i -= 3) {
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s = substr(seq, i, 3)
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if (s in StopModel) break
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if ((s in StartModel) && (StartModel[s] > smax)) {
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imax = i
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smax = StartModel[s]
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}
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}
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if (strand == "-") {
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imax = (imax > 0) ? LenSeq - imax + 1 : imax
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}
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return imax
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}
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#
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function DownStop(pos, strand, _local_, seq, i, imax, s) {
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seq = Seq
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if (strand == "-") {
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pos = LenSeq - pos + 1
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seq = RevSeq
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}
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imax = 0
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for (i = pos ; i < Min(LenSeq, pos+STOP_WALK) ; i += 3) {
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s = substr(seq, i, 3)
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if (s in StopModel) {
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imax = i
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break
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}
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}
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if (strand == "-") {
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imax = (imax > 0) ? LenSeq - imax + 1 : imax
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}
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return imax
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}
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#
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# rules
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#
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BEGIN {
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if (START_MODEL == "") START_MODEL="Models/start.default.frq"
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if (STOP_MODEL == "") STOP_MODEL="Models/stop.default.frq"
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if (START_WALK == "") START_WALK=120
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if (STOP_WALK == "") STOP_WALK=-1
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if (! TestPath(FASTA)) Error("Fasta file: '" FASTA "' not found", 1)
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Seq = tolower(ReadFasta(FASTA))
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LenSeq = length(Seq)
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RevSeq = RevComplement(Seq)
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if (START_WALK < 0) START_WALK = LenSeq
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if (STOP_WALK < 0) STOP_WALK = LenSeq
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if (! TestPath(START_MODEL)) Error("model file: '" START_MODEL "' not found", 2)
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if (! TestPath(STOP_MODEL)) Error("model file: '" STOP_MODEL "' not found", 2)
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ReadModel(START_MODEL, StartModel)
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ReadModel(STOP_MODEL, StopModel)
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}
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#
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/^c begin_entry/ {
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Strand = $7
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nbexon = $9+0
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StartExon = 1 # always first (even on - strand)
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StopExon = nbexon # always last (even on - strand)
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NbExon = 0
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}
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/^c/ {
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print $0
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next
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}
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/^e exon/ {
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NbExon++
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if (NbExon == StartExon) {
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pos = (Strand == "+" ? $3+0 : $4+0)
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start = UpStart(pos, Strand)
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mod_start = (start == 0 ? (Strand == "+" ? "<" : ">") : "=")
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start = (start == 0 ? pos : start)
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$(Strand == "+" ? 3 : 4) = start
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} else {
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mod_start = "="
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}
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if (NbExon == StopExon) {
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pos = (Strand == "+" ? $4+0 : $3+0)
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pos += (Strand == "+" ? 1 : -1)
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stop = DownStop(pos, Strand)
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mod_stop = (stop == 0 ? (Strand == "+" ? ">" : "<") : "=")
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last = (stop == 0 ? pos : stop)
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last += (Strand == "+" ? -1 : 1)
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stop = last + (stop == 0 ? 0 : (Strand == "+") ? 3 : -3)
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$(Strand == "+" ? 4 : 3) = stop
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} else {
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mod_stop = "="
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}
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modif = (Strand == "+" ? mod_start "" mod_stop : mod_stop "" mod_start)
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print $0, "; modifier \"" modif "\""
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next
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}
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/^e (intron|splice|similarity)/ {
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print $0
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next
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}
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