diff --git a/CRISPR.java b/CRISPR.java index 882cffc..23dd9c6 100644 --- a/CRISPR.java +++ b/CRISPR.java @@ -140,7 +140,7 @@ public String toGff(String sequenceName, String parentName) { for (int m = 0; m < numRepeats(); m++) { int repeat_position = (repeatAt(m) + 1); int repeat_end = repeat_position + this.repeatLength() - 1; - str += sequenceName + "\tminced:"+minced.VERSION+"\trepeat_unit\t" + repeat_position + "\t" + repeat_end + "\t1\t.\t.\tParent=" + parentName + ";ID=DR"+(m + 1) + "\n"; + str += sequenceName + "\tminced:"+minced.VERSION+"\trepeat_unit\t" + repeat_position + "\t" + repeat_end + "\t1\t.\t.\tParent=" + parentName + ";ID=DR."+parentName+'.'+(m + 1) + "\n"; } return str; } diff --git a/CRISPRFinder.java b/CRISPRFinder.java index 4e08ed7..354ccd3 100644 --- a/CRISPRFinder.java +++ b/CRISPRFinder.java @@ -298,9 +298,9 @@ private boolean findRepeats( DNASequence sequence, int readNum ) currCRISPR = (CRISPR)CRISPRVector.elementAt(k); if(outputformat > 0) { String crispr_id = "CRISPR" + (++totalCrisprCount); - out.print(sequence.getName() + "\tminced:" + minced.VERSION + "\tCRISPR\t"); + out.print(sequence.getName() + "\tminced:" + minced.VERSION + "\trepeat_region\t"); out.print((currCRISPR.start() + 1) + "\t" + (currCRISPR.end() + 1) + "\t"); - out.print(currCRISPR.numRepeats() + "\t.\t.\tID="+ crispr_id); + out.print(currCRISPR.numRepeats() + "\t.\t.\tID="+ crispr_id + ";rpt_family=CRISPR;rpt_unit_seq="+ currCRISPR.repeatStringAt(1)); out.print("\n"); if(outputformat == 2) { out.print(currCRISPR.toGff(sequence.getName(), crispr_id)); diff --git a/t/Aquifex_aeolicus_VF5.expected b/t/Aquifex_aeolicus_VF5.expected index ad1d2bd..08425f2 100644 --- a/t/Aquifex_aeolicus_VF5.expected +++ b/t/Aquifex_aeolicus_VF5.expected @@ -1,7 +1,7 @@ ##gff-version 3 -gi|15282445|ref|NC_000918.1| minced:0.2.2 CRISPR 156460 156767 5 . . ID=CRISPR1 -gi|15282445|ref|NC_000918.1| minced:0.2.2 CRISPR 244561 244791 4 . . ID=CRISPR2 -gi|15282445|ref|NC_000918.1| minced:0.2.2 CRISPR 279264 279555 5 . . ID=CRISPR3 -gi|15282445|ref|NC_000918.1| minced:0.2.2 CRISPR 1226626 1226861 4 . . ID=CRISPR4 -gi|15282445|ref|NC_000918.1| minced:0.2.2 CRISPR 1379598 1379894 5 . . ID=CRISPR5 -gi|15282445|ref|NC_000918.1| minced:0.2.2 CRISPR 1418900 1419060 3 . . ID=CRISPR6 +gi|15282445|ref|NC_000918.1| minced:0.2.2 repeat_region 156460 156767 5 . . ID=CRISPR1;rpt_family=CRISPR;rpt_unit_seq=GTTCCTAATGTACCGTGTGGAGTTGAAACC +gi|15282445|ref|NC_000918.1| minced:0.2.2 repeat_region 244561 244791 4 . . ID=CRISPR2;rpt_family=CRISPR;rpt_unit_seq=GTTTCAACTCCACACGGTACATTAGGAAC +gi|15282445|ref|NC_000918.1| minced:0.2.2 repeat_region 279264 279555 5 . . ID=CRISPR3;rpt_family=CRISPR;rpt_unit_seq=GTTTTAACTCCACACGGTACATTAGAAAC +gi|15282445|ref|NC_000918.1| minced:0.2.2 repeat_region 1226626 1226861 4 . . ID=CRISPR4;rpt_family=CRISPR;rpt_unit_seq=CGTTTCTAATGTACCGTAGAGGAGTTGAAAC +gi|15282445|ref|NC_000918.1| minced:0.2.2 repeat_region 1379598 1379894 5 . . ID=CRISPR5;rpt_family=CRISPR;rpt_unit_seq=GTTTCAACTCCACTACGGTACATTAGGAAC +gi|15282445|ref|NC_000918.1| minced:0.2.2 repeat_region 1418900 1419060 3 . . ID=CRISPR6;rpt_family=CRISPR;rpt_unit_seq=GTTCCTAATGTACCGTGTGGAGTTGAAAC