First commit - second part
Former-commit-id: 202296404e6a70f8ae96db99faffb456104c57e9 Former-commit-id: 118417735d2055683607df9809c9b721cc1b1bab
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229
detectors/trna/aragorn_wrapper.awk
Executable file
229
detectors/trna/aragorn_wrapper.awk
Executable file
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#!/usr/bin/awk -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 home() {
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"echo $ORGANNOT_HOME" | getline homedir;
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return homedir;
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}
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function prog(program) {
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return home() "/" program;
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}
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function trnalib(prognam) {
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return home() "/lib/trnaCAU.ref.fasta";
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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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if (anticodon == "cat") {
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file=printfasta(trna "_" anticodon,seq,"");
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command= prog("sumatra") " -d -n " file " " trnalib();
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while ((command | getline output) > 0) {
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split(output,field," ");
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n[field[2]]++;
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d[field[2]]=field[3];
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}
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close(command)
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dmin=1;
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for (i in n) {
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dist=d[i]/n[i];
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if (dist < dmin) {
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dmin=dist;
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trna=i;
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}
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}
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}
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else {
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trna="trn" AA1[substr(trna,6,3)];
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}
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return trna;
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}
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function gene2product(gene) {
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return "tRNA-" AA3[substr(gene,4,1)];
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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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print ARGV[1];
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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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trna=patchtRNA(anti,trna,seq);
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# print geneid,trna,loc,anti,"'"intron"'",seq;
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gffTRNA(geneid,trna,loc,anti,intron,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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lseq =$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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trna=patchtRNA(anti,trna,seq);
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# print geneid,trna,loc,anti,"'"intron"'",seq;
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gffTRNA(geneid,trna,loc,anti,intron,seq);
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}
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24
detectors/trna/tools/reannoteCAURefDB.sh
Executable file
24
detectors/trna/tools/reannoteCAURefDB.sh
Executable file
@ -0,0 +1,24 @@
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#!/bin/bash
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SUMATRA=`dirname $0`/sumatra
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function annotateCAU {
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QUERY="$$.query.fasta"
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echo $1 | sed 's/&/ /' | tr '@' '\n' > ${QUERY}
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${SUMATRA} -d -n ${QUERY} $2 2> /dev/null | \
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awk ' {n[$2]+=1;d[$2]+=$3} \
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END {for (i in n) \
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print i, n[i],d[i], d[i]/n[i]\
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}' | \
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sort -rnk4 | \
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egrep '^trn(I|M|fM)' | \
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tail -1 | \
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awk '{print $1,$NF}'
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rm -rf ${QUERY}
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}
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for seq in `awk '(on==1) && /^>/ {print "";on=0} /^>/ {printf("%s@",$0)} ! /^>/ {on=1;printf($0)}' $1 | tr ' ' '&'`; do
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new=(`annotateCAU ${seq} $1`)
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echo $seq | sed 's/&/ /g' | sed -E 's/>([^ ]+) />'${new[0]}' /' | tr '@' '\n'
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done
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