9108ce75f1
Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1 Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984
99 lines
2.2 KiB
Awk
99 lines
2.2 KiB
Awk
#
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#
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#
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function Min(a, b) {
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return (a < b ? a : b)
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}
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function Max(a, b) {
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return (a > b ? a : b)
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}
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function Align(s1, s2, _local_, d, l) {
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if (s1 == s2) return 100
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d = AlignNWS(s1, s2, Identity)
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l = Max(length(s1), length(s2))
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return int((l - d) * 100 / l)
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}
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BEGIN {
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PROCINFO["sorted_in"] = "@ind_num_asc"
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IdentityMatrix("ABCDEFGHIJKLMNOPQRSTUVWXYZ*", Identity)
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}
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BEGINFILE {
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NFile++
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File[NFile] = FILENAME
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}
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/^#/ { next }
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{
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strand = $5
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stop = (strand == "D" ? $4 : $3)
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Stop[stop]++
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i = ++NRec[NFile]
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Rec[NFile][i]["record"] = $0
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Rec[NFile][i]["genefam"] = $1
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Rec[NFile][i]["gene"] = $2
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Rec[NFile][i]["from"] = $3
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Rec[NFile][i]["to"] = $4
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Rec[NFile][i]["strand"] = $5
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Rec[NFile][i]["nexon"] = $6
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Rec[NFile][i]["length"] = $7
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Rec[NFile][i]["protseq"] = $9
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if (NFile == 1)
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Indx1[stop] = i
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else
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Indx2[stop] = i
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}
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END {
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for (st in Stop) {
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if (Indx1[st])
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print "FILE1 " Rec[1][Indx1[st]]["record"]
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else
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print "FILE1 NONE"
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if (Indx2[st])
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print "FILE2 " Rec[2][Indx2[st]]["record"]
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else
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print "FILE2 NONE"
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if (Indx1[st] && Indx2[st]) {
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fm = Rec[1][Indx1[st]]["genefam"]
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id = Align(Rec[1][Indx1[st]]["protseq"], Rec[2][Indx2[st]]["protseq"])
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printf("MATCH %s ID %d ", fm, id)
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if (id == 100)
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status = "CORRECT"
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else if (id >= 90)
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status = "ALMOST_CORRECT"
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else if (id >= 80)
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status = "ACCEPTABLE"
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else
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status = "WRONG"
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if (status != "CORRECT") {
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if (Rec[1][Indx1[st]]["nexon"] != Rec[2][Indx2[st]]["nexon"])
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status = status ".BAD_NBEXON"
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start1 = Rec[1][Indx1[st]]["strand"] == "D" ? Rec[1][Indx1[st]]["from"] : Rec[1][Indx1[st]]["to"]
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start2 = Rec[2][Indx2[st]]["strand"] == "D" ? Rec[2][Indx2[st]]["from"] : Rec[2][Indx2[st]]["to"]
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if (start1 != start2)
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status = status ".BAD_START"
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else
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status = status ".BAD_JUNCTION"
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}
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print status
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}
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else if (Indx1[st]) {
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fm = Rec[1][Indx1[st]]["genefam"]
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print "MATCH " fm " ID 0 MISSED.WRONG_STOP"
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}
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else if (Indx2[st]) {
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fm = Rec[2][Indx2[st]]["genefam"]
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print "MATCH " fm " ID 0 OVERPRED.WRONG_STOP"
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}
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print ""
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}
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}
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