Eric Coissac
f3a045f2ac
Former-commit-id: e5098910d2d5221ccd14b8f840dd12aace06b4d1 Former-commit-id: ea266ab1602753cc926822f34db668049ff193c4
365 lines
8.7 KiB
Awk
Executable File
365 lines
8.7 KiB
Awk
Executable File
#!/usr/bin/env gawk -f
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function genomeid() {
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if (gid=="") {
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gid="XXXXXXX";
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}
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return gid;
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}
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function trnalib() {
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"echo $CAUTRNADB" | getline ref;
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return ref
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}
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function awkPID() {
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"bash -c 'echo $PPID'" | getline pid
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return pid
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}
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function tmpName(prefix,suffix) {
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return prefix awkPID() suffix
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}
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function rm(filename) {
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system("rm -f " filename);
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}
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function printfasta(id,seq,filename) {
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if (filename=="")
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filename = tmpName(id "_",".fasta");
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seqlen=length(seq);
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print ">" id > filename;
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for (i=1; i <= seqlen; i+=60)
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print substr(seq,i,60) >> filename;
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close(filename);
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return filename;
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}
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function epissage(intron,seq) {
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if (intron != "") {
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l=length(intron);
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intron=substr(intron,2,l-2);
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split(intron,intronpos,",");
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lseq=length(seq);
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lintron2=lseq - intronpos[2] + 1;
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seq = substr(seq,1,intronpos[1]) substr(seq,intronpos[2],lintron2);
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}
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return seq;
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}
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function patchtRNA(anticodon,trna,seq) {
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delete res;
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delete maxi;
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delete score;
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delete field;
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delete f2;
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if (anticodon == "cat") {
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file=printfasta(trna "_" anticodon,seq,"");
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command= "sumatra -x -n " file " " trnalib() " 2>> /dev/null";
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while ((command | getline output) > 0) {
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split(output,field," ");
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sub("_"," ",field[2]);
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split(field[2],f2," ");
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trna=f2[1];
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ac=f2[2];
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res[ac][trna]=field[3];
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}
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close(command)
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i=0;
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for (ac in res) {
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max=0;
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for (trna in res[ac]) {
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s=res[ac][trna]
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if (s > max) {
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max=s
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tmax=trna
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}
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}
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i++;
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maxi[tmax][ac]=1
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}
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score["trnfM"]=0;
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score["trnM"]=0;
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score["trnI"]=0;
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for (trna in maxi) {
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score[trna]=length(maxi[trna])
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}
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scores="alternative CAU scores :"
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max=0
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for (trna in score) {
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if (score[trna] > max) {
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max=score[trna];
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tmax=trna;
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}
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scores=scores" "trna"=" score[trna];
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}
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trna=tmax
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}
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else {
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trna="trn" AA1[substr(trna,6,3)];
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scores="-"
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}
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resultat=trna"@"scores
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return resultat;
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}
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function gene2product(gene) {
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return "RNA-" AA3[substr(gene,4,1)];
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}
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function gene2aa(gene,anticodon) {
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aa1=substr(gene,4,1)
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if (aa1=="f") aa1="M"
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if (aa1=="I" && anticodon=="CAU") aa1="M"
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return AA3[aa1];
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}
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function emblTRNA(geneid,trna,loc,anti,antip,intron,notes,seq) {
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if (intron!="") {
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l=length(intron);
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intron=substr(intron,2,l-2);
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split(intron,intronpos,",");
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}
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if (loc ~ /^c/) {
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complement=1;
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match(loc,",[0-9][0-9]*\\]");
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ge=substr(loc,RSTART,RLENGTH);
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match(ge,"[0-9][0-9]*");
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ge=substr(ge,RSTART,RLENGTH);
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sub("c\\[","complement(",loc);
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sub("\\]",")",loc);
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sub(",","..",loc)
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antistart=ge - antip + 1
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antiloc="complement(" antistart - 2 ".." antistart ")"
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if (intron!="") {
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delta = intronpos[1] - antip - 1
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if (delta==1 || delta==2) {
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start= ge - (intronpos[1] + intronpos[2] -1) - 2 + delta
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end= ge - (intronpos[1] + intronpos[2] -1)
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if (start!=end) antie1=start".."end; else antie1=start
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start= ge - intronpos[1] + 2
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end=start + delta - 1
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if (start!=end) antie2=start".."end; else antie2=start
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antiloc="complement(join("antie1","antie2"))"
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}
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}
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}
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else {
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complement=0;
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sub("\\[","",loc);
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sub("\\]","",loc);
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split(loc,locparts,",")
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sub(",","..",loc)
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split(loc,locparts,",")
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sub(",","..",loc)
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antistart=locparts[1]+antip-1
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antiloc=antistart".."(antistart+2)
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if (intron!="") {
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delta = intronpos[1] - antip
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# print delta, intronpos[1], intronpos[2], antip,ge
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if (delta == 1 || delta == 2) {
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start=antistart
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end=antistart + delta - 1
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if (start!=end) antie1=start".."end; else antie1=start
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start=locparts[1] + ( intronpos[1] + intronpos[2] - 1)
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end=start + 2 - delta
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if (start!=end) antie2=start".."end; else antie2=start
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antiloc="join("antie1","antie2")"
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}
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}
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}
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anti=toupper(anti);
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gsub("T","U",anti);
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product=gene2product(trna);
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aa=gene2aa(trna,anti)
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if (intron!="") {
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ib=intronpos[1];
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il=intronpos[2];
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ie=ib+il-1;
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match(loc,"[0-9][0-9]*");
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gb=substr(loc,RSTART,RLENGTH);
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if (complement==0) {
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sub("\\.\\.",".." (gb + ib - 2) "," (gb + ie) "..",loc);
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}
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else {
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sub("\\.\\.",".." (ge - ie) "," (ge - ib + 2) "..",loc);
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}
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sub("complement","complement(join",loc);\
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if (substr(loc,1,1) ~ /[0-9]/) {
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loc="join("loc}
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loc=loc")";
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}
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print "FT tRNA " loc;
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print "FT /gene=\"t" product "(" anti ")\"";
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print "FT /anticodon=(pos:" antiloc ",aa:" aa ",seq:" tolower(anti) ")";
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# print "FT /note=\"*anticodon: "anti"\"";
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print "FT /product=\"transfer " product "(" anti ")\"";
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print "FT /locus_tag=\"\"";
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# print "FT /inference=\"Aragorn-1.2.38\"";
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if (notes!="-")
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print "FT /note=\""notes"\"";
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}
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function gffTRNA(geneid,trna,loc,anti,intron,seq) {
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if (loc ~ /^c/) {
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complement="-";
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loc=substr(loc,3,length(loc)-3);
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}
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else {
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complement="+";
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loc=substr(loc,2,length(loc)-2);
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}
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split(loc,pos,",");
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anti=toupper(anti);
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gsub("T","U",anti);
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product=gene2product(trna);
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printf("%s\taragorn\tgene\t%d\t%d\t.\t%s\t.\tID=genetrn%d;gbkey=Gene;gene=%s\n",
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genomeid(),pos[1],pos[2],complement,geneid,trna);
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printf("%s\taragorn\ttRNA\t%d\t%d\t.\t%s\t.\tID=trn%d;parent=genetrn%d;gbkey=tRNA;gene=%s;Note=anticodon: %s;product=%s\n",
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genomeid(),pos[1],pos[2],complement,geneid,geneid,trna,anti,product);
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if (intron=="") {
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printf("%s\taragorn\texon\t%d\t%d\t.\t%s\t.\tID=exontrn%d;parent=trn%d;gbkey=tRNA;gene=%s;Note=anticodon: %s;product=%s\n",
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genomeid(),pos[1],pos[2],complement,geneid,geneid,trna,anti,product);
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}
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else {
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l=length(intron);
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intron=substr(intron,2,l-2);
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split(intron,intronpos,",");
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lseq=pos[2]-pos[1]+1;
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lintron2=lseq - intronpos[2] + 1;
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seq = substr(seq,1,intronpos[1]) substr(seq,intronpos[2],lintron2);
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printf("%s\taragorn\texon\t%d\t%d\t.\t%s\t.\tID=exontrn%da;parent=trn%d;gbkey=tRNA;gene=%s;Note=anticodon: %s;product=%s\n",
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genomeid(),pos[1],pos[1]+intronpos[1]-2,complement,geneid,geneid,trna,anti,product);
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printf("%s\taragorn\tintron\t%d\t%d\t.\t%s\t.\tID=exontrn%di;parent=trn%d;gbkey=intron;gene=%s;Note=anticodon: %s;product=%s\n",
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genomeid(),pos[1]+intronpos[1]-1,pos[1]+intronpos[2]-2,complement,geneid,geneid,trna,anti,product);
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printf("%s\taragorn\texon\t%d\t%d\t.\t%s\t.\tID=exontrn%db;parent=trn%d;gbkey=tRNA;gene=%s;Note=anticodon: %s;product=%s\n",
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genomeid(),pos[1]+intronpos[2]-1,pos[2],complement,geneid,geneid,trna,anti,product);
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}
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}
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BEGIN {
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AA1["Ala"]="A";
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AA1["Cys"]="C";
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AA1["Asp"]="D";
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AA1["Glu"]="E";
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AA1["Phe"]="F";
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AA1["Gly"]="G";
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AA1["His"]="H";
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AA1["Ile"]="I";
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AA1["Lys"]="K";
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AA1["Leu"]="L";
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AA1["Met"]="M";
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AA1["Asn"]="N";
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AA1["Pyl"]="O";
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AA1["Pro"]="P";
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AA1["Gln"]="Q";
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AA1["Arg"]="R";
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AA1["Ser"]="S";
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AA1["Thr"]="T";
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AA1["Sec"]="U";
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AA1["Val"]="V";
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AA1["Trp"]="W";
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AA1["Tyr"]="Y";
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AA3["A"]="Ala";
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AA3["C"]="Cys";
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AA3["D"]="Asp";
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AA3["E"]="Glu";
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AA3["F"]="Phe";
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AA3["G"]="Gly";
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AA3["H"]="His";
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AA3["I"]="Ile";
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AA3["K"]="Lys";
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AA3["L"]="Leu";
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AA3["M"]="Met";
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AA3["N"]="Asn";
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AA3["O"]="Pyl";
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AA3["P"]="Pro";
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AA3["Q"]="Gln";
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AA3["R"]="Arg";
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AA3["S"]="Ser";
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AA3["T"]="Thr";
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AA3["U"]="Sec";
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AA3["V"]="Val";
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AA3["W"]="Trp";
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AA3["Y"]="Tyr";
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AA3["f"]="fMet";
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}
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/^>/ { id = substr($1,2);
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}
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/^[0-9]+ +genes found/ \
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{ nbgene=$1
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}
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((geneid != "") && /^[0-9]+/ && ! /genes found/) \
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{ seq=epissage(intron,seq);
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xxx=patchtRNA(anti,trna,seq)
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split(xxx,trnadata,"@");
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# print geneid,trna,loc,anti,"'"intron"'",seq;
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emblTRNA(geneid,trnadata[1],loc,anti,antip,intron,trnadata[2],seq);
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seq=""
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}
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/^[0-9]+/ && ! /genes found/ \
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{ geneid=$1;
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trna =$2;
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loc =$3;
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antip =$4;
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x=$5;
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split($5,intron_desc,"i");
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anti =substr(intron_desc[1],2,3);
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intron=intron_desc[2];
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}
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/^[^>0-9]/ \
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{ seq=seq $1
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}
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END { seq=epissage(intron,seq);
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xxx=patchtRNA(anti,trna,seq)
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split(xxx,trnadata,"@");
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# print geneid,trna,loc,anti,"'"intron"'",seq;
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emblTRNA(geneid,trnadata[1],loc,anti,antip,intron,trnadata[2],seq);
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}
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