Eric Coissac
d4da1d01fd
clusterizecore.sh script from the detectors/cds/lib folder. The CDS detector is now modified to use the clean.fst files. Former-commit-id: e30a53b5b6b658388af4b2640b30e6765c729894 Former-commit-id: 3015ad50d25248fb117ab00e816b00fde1f9ba1d
134 lines
2.6 KiB
Awk
134 lines
2.6 KiB
Awk
#
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# select best cluster(s)
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#
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# -v MAX_SPAN ALLOW_STOP EXCLUDE
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#
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#
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#
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BEGIN {
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PROCINFO["sorted_in"] = "@ind_num_asc"
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if (MAX_SPAN == "") MAX_SPAN = 10000
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if (ALLOW_STOP == "") ALLOW_STOP = 0
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if (EXCLUDE == "") EXCLUDE = 0
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}
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/^\# --- START OF GFF DUMP ---/ {
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State = "gff"
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NbEntry++
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next
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}
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/^\# --- END OF GFF DUMP ---/ {
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State = 0
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next
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}
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/^C4 Alignment:/ {
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for (i = 1 ; i <= 8 ; i++)
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getline
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State = "align"
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Align = ""
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next
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}
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/^\#/ { next }
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(State == 0) { next }
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(State == "gff") && ($3 == "gene") {
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span = $5 - $4 + 1
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valid = (span < MAX_SPAN) \
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&& (ALLOW_STOP || (Align !~ "\\*")) \
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&& ((EXCLUDE == 0) || (! (Organism ~ EXCLUDE)))
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Entry[NbEntry]["valid"] = valid
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Entry[NbEntry]["from"] = $4+0
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Entry[NbEntry]["to"] = $5+0
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Entry[NbEntry]["score"] = $6+0
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Entry[NbEntry]["strand"] = $7
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if (valid) {
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for (i = $4+0 ; i <= $5+0; i++)
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Cover[i] = 1
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}
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}
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(State == "gff") && ($3 == "exon") {
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Entry[NbEntry]["nbexon"]++
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}
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(State == "gff") {
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n = ++Entry[NbEntry]["nbline"]
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$1=$2=""
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Entry[NbEntry][n] = $0
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}
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(State == "align") && /^vulgar/ {
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State = 0
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split($2, a, "@")
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Organism = a[1]
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next
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}
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(State == "align") {
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getline; getline
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Align = Align "" $0
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getline; getline
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next
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}
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END {
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# make clusters
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pi = -1
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for (i in Cover) {
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if (i+0 > pi+1)
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Clust[++NbClust]["from"] = i
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pi = Clust[NbClust]["to"] = i
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}
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# get highest scoring clusters
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for (i = 1 ; i <= NbEntry ; i++) {
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valid = Entry[i]["valid"]
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if (! valid) continue
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clusno = 0
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for (j = 1; j <= NbClust; j++) {
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if ((Entry[i]["from"] >= Clust[j]["from"]) && (Entry[i]["to"] <= Clust[j]["to"]))
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clusno = j
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}
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valid = (clusno != 0)
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if (! valid) continue
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score = Entry[i]["score"]
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if (score > Clust[clusno]["score"]+0) {
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Clust[clusno]["score"] = score
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Clust[clusno]["strand"] = Entry[i]["strand"]
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Clust[clusno]["entry"] = i
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}
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}
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# print cluster info
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print "c nclust", NbClust+0
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for (i = 1 ; i <= NbClust ; i++) {
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print "c cluster", i, "from", Clust[i]["from"], "to", Clust[i]["to"],\
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"strand", Clust[i]["strand"], "score", Clust[i]["score"]
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}
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# print best clusters
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for (i = 1 ; i <= NbClust ; i++) {
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if (Clust[i]["score"] == 0) continue
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j = Clust[i]["entry"]
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s = Clust[i]["strand"]
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n = Entry[j]["nbline"]
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ne = Entry[j]["nbexon"]
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print "c begin_entry", j, "cluster", i, "strand", s, "nbexon", ne
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for (k = 1 ; k <= n ; k++) {
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entry = Entry[j][k]
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gsub("^ +", "", entry)
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print "e", entry
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}
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print "c end_entry", j, "cluster", i
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}
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}
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