97 lines
1.9 KiB
Awk
97 lines
1.9 KiB
Awk
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#
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# get intron features from genbank
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#
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# @include libgbk.awk
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BEGIN {
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print "#locus locustag genefam gene from to strand intron_num intron_nb acceptor-donor status"
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if (HEADONLY != "") exit(0)
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if (FASTA == "") Error("No FASTA file specified", 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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}
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/^LOCUS/ {
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locus = $2
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next
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}
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/^ CDS/ {
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revstrand = match($2, "^complement")
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s = substr($0, 22)
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gsub("^complement", "", s)
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ok = ! match(s, "complement|order")
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if (! ok) next
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na = ParseLocation(s, locs)
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if (na < 2) next
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delete SINfo
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Ninfo = 0
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val = locs[1][1]
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for (i = 2 ; i <= na ; i++) {
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if (locs[i][1] < val) ok = 0
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val = locs[i][1]
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}
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if (! ok) next
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val = locs[1][2]
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for (i = 2 ; i <= na ; i++) {
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if (locs[i][2] < val) ok = 0
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val = locs[i][2]
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}
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if (! ok) next
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from = locs[1][2] + 1
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for (i = 2 ; i <= na ; i++) {
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to = locs[i][1] - 1
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inseq = SeqLocation(Seq, (from - 4) ".." (to + 4), revstrand)
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SINfo[++Ninfo] = from " " to " " (revstrand ? "R" : "D") " "\
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(revstrand ? na-i+1 : i-1) " " na-1 " "\
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substr(inseq, 1,4) "."\
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substr(inseq, 5,6) "-"\
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substr(inseq, length(inseq)-9, 6) "."\
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substr(inseq, length(inseq)-3, 4) " "\
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"ok"
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from = locs[i][2] + 1
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}
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gene = "none"
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locustag = "none"
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next
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}
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/^ \/gene=/ {
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split($0, a, "=")
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gene = a[2]
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gsub("^[^a-z,A-Z]+", "", gene)
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gsub("\"", "", gene)
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gsub(" ", "_", gene)
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next
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}
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/^ \/locus_tag=/ {
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split($0, a, "=")
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locustag = a[2]
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gsub("\"", "", locustag)
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gsub(" ", "_", locustag)
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next
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}
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/^ \/translation=/ {
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for (i = 1 ; i <= Ninfo ; i++)
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print locus, locustag, GeneFamily(gene), gene, SINfo[i]
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Ninfo = 0
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next
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}
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/^\/\// {
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locus = "?"
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}
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