diff --git a/detectors/cds/bin/do_rps12.sh b/detectors/cds/bin/do_rps12.sh index e07a412..39239b7 100755 --- a/detectors/cds/bin/do_rps12.sh +++ b/detectors/cds/bin/do_rps12.sh @@ -264,9 +264,9 @@ blastx \ export PASS1_SPEEDUP=0 cp $DBROOT/Annot.lst RPS12 - for f in rps12_fragments_*.fasta ; do + for fasta in rps12_fragments_*.fasta ; do tcsh -f ${PROG_DIR}/do_exonerate.csh \ - $f \ + $fasta \ "RPS12/rps12.fasta" \ $DBROOT/../models $(pwd) done diff --git a/detectors/cds/lib/toEmbl.awk b/detectors/cds/lib/toEmbl.awk index 73983ff..eebf5f5 100644 --- a/detectors/cds/lib/toEmbl.awk +++ b/detectors/cds/lib/toEmbl.awk @@ -191,23 +191,23 @@ function Unk(s) { } - if (Nexon > 1) { - for (i = 1 ; i <= Nexon ; i++) { - Feature("exon", ExonLocation(i)) - QQualifier("gene", gname) - QQualifier("locus_tag", locus) + # if (Nexon > 1) { + # for (i = 1 ; i <= Nexon ; i++) { + # Feature("exon", ExonLocation(i)) + # QQualifier("gene", gname) + # QQualifier("locus_tag", locus) - if (Exon[i]["frameshift"]) { - QQualifier("pseudogene","unknown") - if (Exon[i]["frameshift"] > 0) - QQualifier("note","frameshifted by insertion of " Exon[i]["frameshift"] " bp") - else - QQualifier("note","frameshifted by deletion of " -Exon[i]["frameshift"] " bp") - } + # if (Exon[i]["frameshift"]) { + # QQualifier("pseudogene","unknown") + # if (Exon[i]["frameshift"] > 0) + # QQualifier("note","frameshifted by insertion of " Exon[i]["frameshift"] " bp") + # else + # QQualifier("note","frameshifted by deletion of " -Exon[i]["frameshift"] " bp") + # } - SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1) - } - } + # SQualifier("number", Exon[1]["strand"] == "+" ? i : Nexon-i+1) + # } + # } }