[galaxy-dev] [hg] galaxy 1525: Modified INDEL tools under Regional variation ...

24 Sep 2008

details:   http://www.bx.psu.edu/hg/galaxy/rev/675ad84ae008
changeset: 1525:675ad84ae008
user:      guru
date:      Mon Sep 22 12:02:35 2008 -0400
description:
Modified INDEL tools under Regional variation section.

6 file(s) affected in this change:

test-data/indelrates_3way.tabular
test-data/indels_3way.tabular
tools/regVariation/getIndelRates_3way.py
tools/regVariation/getIndelRates_3way.xml
tools/regVariation/getIndels_3way.xml
tools/regVariation/parseMAF_smallIndels.pl

diffs (908 lines):

diff -r aae4754d6828 -r 675ad84ae008 test-data/indelrates_3way.tabular

--- a/test-data/indelrates_3way.tabular	Mon Sep 22 10:36:34 2008 -0400
+++ b/test-data/indelrates_3way.tabular	Mon Sep 22 12:02:35 2008 -0400
@@ -1,13 +1,15 @@
-#Window	Species	Window_Start	Window_End	Insertion_Rate	Deletion_Rate
-1	canFam2	3356001	3357001	3.80e-03	2.17e-03
-2	canFam2	3357001	3358001	2.46e-03	1.85e-03
-3	canFam2	3358001	3359001	1.23e-03	3.08e-03
-4	canFam2	3359001	3360001	6.76e-03	8.39e-03
-5	canFam2	3360001	3361001	8.41e-03	1.12e-02
-6	canFam2	3361001	3362001	9.27e-03	1.85e-02
-7	canFam2	3362001	3363001	1.17e-02	6.67e-03
-8	canFam2	3363001	3364001	1.97e-02	5.62e-03
-9	canFam2	3364001	3365001	5.92e-03	9.65e-03
-10	canFam2	3366001	3367001	3.69e-03	2.63e-03
-11	canFam2	3367001	3368001	9.89e-03	4.95e-03
-12	canFam2	3368001	3369001	6.90e-03	1.38e-02
+#Block	hg18_InsRate	panTro2_InsRate	canFam2_InsRate	hg18_DelRate	panTro2_DelRate	canFam2_DelRate
+1	0.00e+00	6.90e-03	6.90e-03	0.00e+00	0.00e+00	1.38e-02
+2	0.00e+00	0.00e+00	1.27e-02	7.25e-04	0.00e+00	6.36e-03
+3	0.00e+00	0.00e+00	6.21e-03	0.00e+00	0.00e+00	6.21e-03
+4	0.00e+00	0.00e+00	2.07e-02	0.00e+00	0.00e+00	5.18e-03
+5	0.00e+00	0.00e+00	2.54e-02	0.00e+00	0.00e+00	1.69e-02
+6	0.00e+00	0.00e+00	9.61e-04	0.00e+00	0.00e+00	0.00e+00
+7	0.00e+00	0.00e+00	1.97e-02	0.00e+00	0.00e+00	5.62e-03
+8	0.00e+00	1.71e-03	1.17e-02	0.00e+00	1.71e-03	6.67e-03
+9	0.00e+00	0.00e+00	1.05e-02	2.72e-03	0.00e+00	1.83e-02
+10	0.00e+00	3.26e-03	1.51e-02	0.00e+00	0.00e+00	1.89e-02
+12	1.25e-03	0.00e+00	8.70e-03	0.00e+00	0.00e+00	1.24e-02
+13	0.00e+00	0.00e+00	6.76e-03	0.00e+00	0.00e+00	4.73e-02
+14	0.00e+00	0.00e+00	4.93e-03	1.23e-03	1.23e-03	5.55e-03
+15	0.00e+00	0.00e+00	2.29e-02	0.00e+00	0.00e+00	1.38e-02
diff -r aae4754d6828 -r 675ad84ae008 test-data/indels_3way.tabular
--- a/test-data/indels_3way.tabular	Mon Sep 22 10:36:34 2008 -0400
+++ b/test-data/indels_3way.tabular	Mon Sep 22 12:02:35 2008 -0400
@@ -1,149 +1,149 @@
-#block	indel_type	indel_length	ingroup1	ingroup1_start	ingroup1_end	ingroup1_orient	ingroup2	ingroup2_start	ingroup2_end	ingroup2_orient	outgroup	outgroup_start	outgroup_end	outgroup_orient
-12	hg18.chr1:802_insert	1	hg18.chr1:802	57213	57213	+	panTro2.chrUn:801	9724391	9724392	+	canFam2.chr30:805	3360548	3360549	-
-2	hg18.chr1:1380_delete	4	hg18.chr1:1380	48103	48104	+	panTro2.chrUn:1384	9713713	9713716	+	canFam2.chr30:1415	3367755	3367758	-
-9	hg18.chr1:367_delete	35	hg18.chr1:367	55389	55390	+	panTro2.chrUn:402	9721584	9721618	+	canFam2.chr30:382	3361661	3361695	-
-14	hg18.chr1:1628_delete	1	hg18.chr1:1628	58770	58771	+	panTro2.chrUn:1631	9725949	9725949	+	canFam2.chr30:1623	3357056	3357056	-
-14	hg18.chr1:1628_delete	4	hg18.chr1:1628	58770	58771	+	panTro2.chrUn:1631	9725950	9725953	+	canFam2.chr30:1623	3357058	3357061	-
-1	panTro2.chrUn:145_insert	2	hg18.chr1:143	46857	46858	+	panTro2.chrUn:145	9712465	9712466	+	canFam2.chr30:145	3368190	3368191	-
-8	panTro2.chrUn:585_insert	4	hg18.chr1:582	54744	54745	+	panTro2.chrUn:585	9720936	9720939	+	canFam2.chr30:600	3362635	3362636	-
-10	panTro2.chrUn:307_insert	35	hg18.chr1:272	55984	55985	+	panTro2.chrUn:307	9721981	9722015	+	canFam2.chr30:265	3361105	3361106	-
-8	panTro2.chrUn:585_delete	1	hg18.chr1:582	54979	54979	+	panTro2.chrUn:585	9721173	9721174	+	canFam2.chr30:600	3362890	3362890	-
-14	panTro2.chrUn:1631_delete	1	hg18.chr1:1628	59015	59015	+	panTro2.chrUn:1631	9726197	9726198	+	canFam2.chr30:1623	3357328	3357328	-
-14	panTro2.chrUn:1631_delete	1	hg18.chr1:1628	60211	60211	+	panTro2.chrUn:1631	9727392	9727393	+	canFam2.chr30:1623	3358490	3358490	-
-1	canFam2.chr30:145_insert	4	hg18.chr1:143	46796	46797	+	panTro2.chrUn:145	9712403	9712404	+	canFam2.chr30:145	3368127	3368130	-
-2	canFam2.chr30:1415_insert	8	hg18.chr1:1380	47138	47139	+	panTro2.chrUn:1384	9712747	9712748	+	canFam2.chr30:1415	3366730	3366737	-
-2	canFam2.chr30:1415_insert	3	hg18.chr1:1380	47263	47264	+	panTro2.chrUn:1384	9712872	9712873	+	canFam2.chr30:1415	3366862	3366864	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	47293	47294	+	panTro2.chrUn:1384	9712902	9712903	+	canFam2.chr30:1415	3366895	3366895	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	47312	47313	+	panTro2.chrUn:1384	9712921	9712922	+	canFam2.chr30:1415	3366915	3366915	-
-2	canFam2.chr30:1415_insert	7	hg18.chr1:1380	47440	47441	+	panTro2.chrUn:1384	9713049	9713050	+	canFam2.chr30:1415	3367044	3367050	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	47528	47529	+	panTro2.chrUn:1384	9713137	9713138	+	canFam2.chr30:1415	3367138	3367138	-
-2	canFam2.chr30:1415_insert	10	hg18.chr1:1380	47546	47547	+	panTro2.chrUn:1384	9713155	9713156	+	canFam2.chr30:1415	3367157	3367166	-
-2	canFam2.chr30:1415_insert	4	hg18.chr1:1380	47562	47563	+	panTro2.chrUn:1384	9713171	9713172	+	canFam2.chr30:1415	3367183	3367186	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	47648	47649	+	panTro2.chrUn:1384	9713257	9713258	+	canFam2.chr30:1415	3367273	3367273	-
-2	canFam2.chr30:1415_insert	3	hg18.chr1:1380	47672	47673	+	panTro2.chrUn:1384	9713281	9713282	+	canFam2.chr30:1415	3367298	3367300	-
-2	canFam2.chr30:1415_insert	5	hg18.chr1:1380	47734	47735	+	panTro2.chrUn:1384	9713343	9713344	+	canFam2.chr30:1415	3367361	3367365	-
-2	canFam2.chr30:1415_insert	2	hg18.chr1:1380	47759	47760	+	panTro2.chrUn:1384	9713368	9713369	+	canFam2.chr30:1415	3367391	3367392	-
-2	canFam2.chr30:1415_insert	2	hg18.chr1:1380	47835	47836	+	panTro2.chrUn:1384	9713444	9713445	+	canFam2.chr30:1415	3367469	3367470	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	48017	48018	+	panTro2.chrUn:1384	9713626	9713627	+	canFam2.chr30:1415	3367653	3367653	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	48035	48036	+	panTro2.chrUn:1384	9713644	9713645	+	canFam2.chr30:1415	3367672	3367672	-
-2	canFam2.chr30:1415_insert	4	hg18.chr1:1380	48091	48092	+	panTro2.chrUn:1384	9713700	9713701	+	canFam2.chr30:1415	3367729	3367732	-
-2	canFam2.chr30:1415_insert	10	hg18.chr1:1380	48103	48104	+	panTro2.chrUn:1384	9713712	9713713	+	canFam2.chr30:1415	3367745	3367754	-
-2	canFam2.chr30:1415_insert	1	hg18.chr1:1380	48232	48233	+	panTro2.chrUn:1384	9713845	9713846	+	canFam2.chr30:1415	3367870	3367870	-
-3	canFam2.chr30:483_insert	15	hg18.chr1:455	48379	48380	+	panTro2.chrUn:455	9714289	9714290	+	canFam2.chr30:483	3366038	3366052	-
-3	canFam2.chr30:483_insert	21	hg18.chr1:455	48426	48427	+	panTro2.chrUn:455	9714336	9714337	+	canFam2.chr30:483	3366096	3366116	-
-3	canFam2.chr30:483_insert	1	hg18.chr1:455	48523	48524	+	panTro2.chrUn:455	9714433	9714434	+	canFam2.chr30:483	3366213	3366213	-
-4	canFam2.chr30:193_insert	8	hg18.chr1:183	52535	52536	+	panTro2.chrUn:183	9718438	9718439	+	canFam2.chr30:193	3364655	3364662	-
-4	canFam2.chr30:193_insert	1	hg18.chr1:183	52555	52556	+	panTro2.chrUn:183	9718458	9718459	+	canFam2.chr30:193	3364683	3364683	-
-4	canFam2.chr30:193_insert	1	hg18.chr1:183	52588	52589	+	panTro2.chrUn:183	9718491	9718492	+	canFam2.chr30:193	3364717	3364717	-
-4	canFam2.chr30:193_insert	4	hg18.chr1:183	52691	52692	+	panTro2.chrUn:183	9718594	9718595	+	canFam2.chr30:193	3364817	3364820	-
-5	canFam2.chr30:118_insert	3	hg18.chr1:115	52709	52710	+	panTro2.chrUn:115	9718612	9718613	+	canFam2.chr30:118	3364525	3364527	-
-5	canFam2.chr30:118_insert	1	hg18.chr1:115	52754	52755	+	panTro2.chrUn:115	9718657	9718658	+	canFam2.chr30:118	3364571	3364571	-
-5	canFam2.chr30:118_insert	4	hg18.chr1:115	52763	52764	+	panTro2.chrUn:115	9718666	9718667	+	canFam2.chr30:118	3364581	3364584	-
-6	canFam2.chr30:1041_insert	1	hg18.chr1:1040	53848	53849	+	panTro2.chrUn:1040	9719751	9719752	+	canFam2.chr30:1041	3364511	3364511	-
-7	canFam2.chr30:356_insert	4	hg18.chr1:335	53869	53870	+	panTro2.chrUn:335	9719772	9719773	+	canFam2.chr30:356	3363136	3363139	-
-7	canFam2.chr30:356_insert	1	hg18.chr1:335	53899	53900	+	panTro2.chrUn:335	9719802	9719803	+	canFam2.chr30:356	3363168	3363168	-
-7	canFam2.chr30:356_insert	1	hg18.chr1:335	53921	53922	+	panTro2.chrUn:335	9719824	9719825	+	canFam2.chr30:356	3363191	3363191	-
-7	canFam2.chr30:356_insert	8	hg18.chr1:335	53938	53939	+	panTro2.chrUn:335	9719841	9719842	+	canFam2.chr30:356	3363209	3363216	-
-7	canFam2.chr30:356_insert	7	hg18.chr1:335	53970	53971	+	panTro2.chrUn:335	9719873	9719874	+	canFam2.chr30:356	3363249	3363255	-
-7	canFam2.chr30:356_insert	5	hg18.chr1:335	54101	54102	+	panTro2.chrUn:335	9720004	9720005	+	canFam2.chr30:356	3363383	3363387	-
-7	canFam2.chr30:356_insert	1	hg18.chr1:335	54164	54165	+	panTro2.chrUn:335	9720067	9720068	+	canFam2.chr30:356	3363451	3363451	-
-8	canFam2.chr30:600_insert	1	hg18.chr1:582	54579	54580	+	panTro2.chrUn:585	9720770	9720771	+	canFam2.chr30:600	3362472	3362472	-
-8	canFam2.chr30:600_insert	1	hg18.chr1:582	54654	54655	+	panTro2.chrUn:585	9720845	9720846	+	canFam2.chr30:600	3362547	3362547	-
-8	canFam2.chr30:600_insert	1	hg18.chr1:582	54691	54692	+	panTro2.chrUn:585	9720882	9720883	+	canFam2.chr30:600	3362585	3362585	-
-8	canFam2.chr30:600_insert	18	hg18.chr1:582	54775	54776	+	panTro2.chrUn:585	9720970	9720971	+	canFam2.chr30:600	3362667	3362684	-
-8	canFam2.chr30:600_insert	1	hg18.chr1:582	54799	54800	+	panTro2.chrUn:585	9720994	9720995	+	canFam2.chr30:600	3362709	3362709	-
-8	canFam2.chr30:600_insert	4	hg18.chr1:582	54944	54945	+	panTro2.chrUn:585	9721139	9721140	+	canFam2.chr30:600	3362851	3362854	-
-8	canFam2.chr30:600_insert	1	hg18.chr1:582	54969	54970	+	panTro2.chrUn:585	9721164	9721165	+	canFam2.chr30:600	3362880	3362880	-
-9	canFam2.chr30:382_insert	1	hg18.chr1:367	55360	55361	+	panTro2.chrUn:402	9721554	9721555	+	canFam2.chr30:382	3361632	3361632	-
-9	canFam2.chr30:382_insert	1	hg18.chr1:367	55378	55379	+	panTro2.chrUn:402	9721572	9721573	+	canFam2.chr30:382	3361651	3361651	-
-9	canFam2.chr30:382_insert	1	hg18.chr1:367	55396	55397	+	panTro2.chrUn:402	9721625	9721626	+	canFam2.chr30:382	3361703	3361703	-
-9	canFam2.chr30:382_insert	2	hg18.chr1:367	55444	55445	+	panTro2.chrUn:402	9721673	9721674	+	canFam2.chr30:382	3361752	3361753	-
-10	canFam2.chr30:265_insert	1	hg18.chr1:272	55776	55777	+	panTro2.chrUn:307	9721772	9721773	+	canFam2.chr30:265	3360902	3360902	-
-10	canFam2.chr30:265_insert	5	hg18.chr1:272	55864	55865	+	panTro2.chrUn:307	9721860	9721861	+	canFam2.chr30:265	3360991	3360995	-
-10	canFam2.chr30:265_insert	2	hg18.chr1:272	55969	55970	+	panTro2.chrUn:307	9721965	9721966	+	canFam2.chr30:265	3361087	3361088	-
-10	canFam2.chr30:265_insert	2	hg18.chr1:272	55980	55981	+	panTro2.chrUn:307	9721976	9721977	+	canFam2.chr30:265	3361100	3361101	-
-12	canFam2.chr30:805_insert	33	hg18.chr1:802	56722	56723	+	panTro2.chrUn:801	9723901	9723902	+	canFam2.chr30:805	3360035	3360067	-
-12	canFam2.chr30:805_insert	1	hg18.chr1:802	56746	56747	+	panTro2.chrUn:801	9723925	9723926	+	canFam2.chr30:805	3360092	3360092	-
-12	canFam2.chr30:805_insert	1	hg18.chr1:802	56836	56837	+	panTro2.chrUn:801	9724015	9724016	+	canFam2.chr30:805	3360183	3360183	-
-12	canFam2.chr30:805_insert	1	hg18.chr1:802	56864	56865	+	panTro2.chrUn:801	9724043	9724044	+	canFam2.chr30:805	3360212	3360212	-
-12	canFam2.chr30:805_insert	1	hg18.chr1:802	56894	56895	+	panTro2.chrUn:801	9724073	9724074	+	canFam2.chr30:805	3360243	3360243	-
-12	canFam2.chr30:805_insert	2	hg18.chr1:802	57161	57162	+	panTro2.chrUn:801	9724340	9724341	+	canFam2.chr30:805	3360496	3360497	-
-12	canFam2.chr30:805_insert	1	hg18.chr1:802	57352	57353	+	panTro2.chrUn:801	9724530	9724531	+	canFam2.chr30:805	3360680	3360680	-
-13	canFam2.chr30:148_insert	2	hg18.chr1:176	58529	58530	+	panTro2.chrUn:176	9725707	9725708	+	canFam2.chr30:148	3359565	3359566	-
-14	canFam2.chr30:1623_insert	1	hg18.chr1:1628	58700	58701	+	panTro2.chrUn:1631	9725878	9725879	+	canFam2.chr30:1623	3356984	3356984	-
-14	canFam2.chr30:1623_insert	1	hg18.chr1:1628	58709	58710	+	panTro2.chrUn:1631	9725887	9725888	+	canFam2.chr30:1623	3356994	3356994	-
-14	canFam2.chr30:1623_insert	1	hg18.chr1:1628	58770	58771	+	panTro2.chrUn:1631	9725949	9725950	+	canFam2.chr30:1623	3357057	3357057	-
-14	canFam2.chr30:1623_insert	1	hg18.chr1:1628	58772	58773	+	panTro2.chrUn:1631	9725955	9725956	+	canFam2.chr30:1623	3357064	3357064	-
-14	canFam2.chr30:1623_insert	15	hg18.chr1:1628	58800	58801	+	panTro2.chrUn:1631	9725983	9725984	+	canFam2.chr30:1623	3357093	3357107	-
-14	canFam2.chr30:1623_insert	9	hg18.chr1:1628	58808	58809	+	panTro2.chrUn:1631	9725991	9725992	+	canFam2.chr30:1623	3357116	3357124	-
-14	canFam2.chr30:1623_insert	1	hg18.chr1:1628	60032	60033	+	panTro2.chrUn:1631	9727214	9727215	+	canFam2.chr30:1623	3358319	3358319	-
-14	canFam2.chr30:1623_insert	4	hg18.chr1:1628	60148	60149	+	panTro2.chrUn:1631	9727330	9727331	+	canFam2.chr30:1623	3358426	3358429	-
-15	canFam2.chr30:218_insert	1	hg18.chr1:230	60326	60327	+	panTro2.chrUn:230	9727507	9727508	+	canFam2.chr30:218	3356643	3356643	-
-15	canFam2.chr30:218_insert	2	hg18.chr1:230	60353	60354	+	panTro2.chrUn:230	9727534	9727535	+	canFam2.chr30:218	3356671	3356672	-
-15	canFam2.chr30:218_insert	1	hg18.chr1:230	60391	60392	+	panTro2.chrUn:230	9727572	9727573	+	canFam2.chr30:218	3356711	3356711	-
-15	canFam2.chr30:218_insert	1	hg18.chr1:230	60466	60467	+	panTro2.chrUn:230	9727647	9727648	+	canFam2.chr30:218	3356783	3356783	-
-15	canFam2.chr30:218_insert	5	hg18.chr1:230	60476	60477	+	panTro2.chrUn:230	9727657	9727658	+	canFam2.chr30:218	3356794	3356798	-
-1	canFam2.chr30:145_delete	1	hg18.chr1:143	46857	46857	+	panTro2.chrUn:145	9712464	9712464	+	canFam2.chr30:145	3368190	3368191	-
-1	canFam2.chr30:145_delete	1	hg18.chr1:143	46900	46900	+	panTro2.chrUn:145	9712509	9712509	+	canFam2.chr30:145	3368232	3368233	-
-2	canFam2.chr30:1415_delete	7	hg18.chr1:1380	47080	47086	+	panTro2.chrUn:1384	9712689	9712695	+	canFam2.chr30:1415	3366677	3366678	-
-2	canFam2.chr30:1415_delete	1	hg18.chr1:1380	47168	47168	+	panTro2.chrUn:1384	9712777	9712777	+	canFam2.chr30:1415	3366766	3366767	-
-2	canFam2.chr30:1415_delete	1	hg18.chr1:1380	47482	47482	+	panTro2.chrUn:1384	9713091	9713091	+	canFam2.chr30:1415	3367091	3367092	-
-2	canFam2.chr30:1415_delete	2	hg18.chr1:1380	47703	47704	+	panTro2.chrUn:1384	9713312	9713313	+	canFam2.chr30:1415	3367330	3367331	-
-2	canFam2.chr30:1415_delete	15	hg18.chr1:1380	48139	48153	+	panTro2.chrUn:1384	9713752	9713766	+	canFam2.chr30:1415	3367793	3367794	-
-2	canFam2.chr30:1415_delete	1	hg18.chr1:1380	48160	48160	+	panTro2.chrUn:1384	9713773	9713773	+	canFam2.chr30:1415	3367799	3367800	-
-2	canFam2.chr30:1415_delete	1	hg18.chr1:1380	48174	48174	+	panTro2.chrUn:1384	9713787	9713787	+	canFam2.chr30:1415	3367812	3367813	-
-2	canFam2.chr30:1415_delete	1	hg18.chr1:1380	48197	48197	+	panTro2.chrUn:1384	9713810	9713810	+	canFam2.chr30:1415	3367834	3367835	-
-2	canFam2.chr30:1415_delete	5	hg18.chr1:1380	48280	48284	+	panTro2.chrUn:1384	9713893	9713897	+	canFam2.chr30:1415	3367917	3367918	-
-3	canFam2.chr30:483_delete	4	hg18.chr1:455	48344	48347	+	panTro2.chrUn:455	9714254	9714257	+	canFam2.chr30:483	3366005	3366006	-
-3	canFam2.chr30:483_delete	4	hg18.chr1:455	48410	48413	+	panTro2.chrUn:455	9714320	9714323	+	canFam2.chr30:483	3366082	3366083	-
-3	canFam2.chr30:483_delete	1	hg18.chr1:455	48470	48470	+	panTro2.chrUn:455	9714380	9714380	+	canFam2.chr30:483	3366159	3366160	-
-4	canFam2.chr30:193_delete	4	hg18.chr1:183	52639	52642	+	panTro2.chrUn:183	9718542	9718545	+	canFam2.chr30:193	3364767	3364768	-
-5	canFam2.chr30:118_delete	3	hg18.chr1:115	52707	52709	+	panTro2.chrUn:115	9718610	9718612	+	canFam2.chr30:118	3364524	3364525	-
-5	canFam2.chr30:118_delete	2	hg18.chr1:115	52743	52744	+	panTro2.chrUn:115	9718646	9718647	+	canFam2.chr30:118	3364560	3364561	-
-7	canFam2.chr30:356_delete	2	hg18.chr1:335	53879	53880	+	panTro2.chrUn:335	9719782	9719783	+	canFam2.chr30:356	3363148	3363149	-
-7	canFam2.chr30:356_delete	4	hg18.chr1:335	54052	54055	+	panTro2.chrUn:335	9719955	9719958	+	canFam2.chr30:356	3363336	3363337	-
-8	canFam2.chr30:600_delete	1	hg18.chr1:582	54634	54634	+	panTro2.chrUn:585	9720825	9720825	+	canFam2.chr30:600	3362526	3362527	-
-8	canFam2.chr30:600_delete	3	hg18.chr1:582	54710	54712	+	panTro2.chrUn:585	9720901	9720903	+	canFam2.chr30:600	3362603	3362604	-
-8	canFam2.chr30:600_delete	4	hg18.chr1:582	54876	54879	+	panTro2.chrUn:585	9721071	9721074	+	canFam2.chr30:600	3362785	3362786	-
-8	canFam2.chr30:600_delete	1	hg18.chr1:582	54984	54984	+	panTro2.chrUn:585	9721178	9721178	+	canFam2.chr30:600	3362894	3362895	-
-9	canFam2.chr30:382_delete	1	hg18.chr1:367	55131	55131	+	panTro2.chrUn:402	9721325	9721325	+	canFam2.chr30:382	3361420	3361421	-
-9	canFam2.chr30:382_delete	6	hg18.chr1:367	55213	55218	+	panTro2.chrUn:402	9721407	9721412	+	canFam2.chr30:382	3361501	3361502	-
-9	canFam2.chr30:382_delete	1	hg18.chr1:367	55308	55308	+	panTro2.chrUn:402	9721502	9721502	+	canFam2.chr30:382	3361590	3361591	-
-9	canFam2.chr30:382_delete	4	hg18.chr1:367	55324	55327	+	panTro2.chrUn:402	9721518	9721521	+	canFam2.chr30:382	3361605	3361606	-
-9	canFam2.chr30:382_delete	7	hg18.chr1:367	55340	55346	+	panTro2.chrUn:402	9721534	9721540	+	canFam2.chr30:382	3361617	3361618	-
-9	canFam2.chr30:382_delete	2	hg18.chr1:367	55386	55387	+	panTro2.chrUn:402	9721580	9721581	+	canFam2.chr30:382	3361658	3361659	-
-9	canFam2.chr30:382_delete	4	hg18.chr1:367	55457	55460	+	panTro2.chrUn:402	9721686	9721689	+	canFam2.chr30:382	3361765	3361766	-
-10	canFam2.chr30:265_delete	11	hg18.chr1:272	55893	55903	+	panTro2.chrUn:307	9721889	9721899	+	canFam2.chr30:265	3361023	3361024	-
-10	canFam2.chr30:265_delete	1	hg18.chr1:272	55924	55924	+	panTro2.chrUn:307	9721920	9721920	+	canFam2.chr30:265	3361043	3361044	-
-10	canFam2.chr30:265_delete	1	hg18.chr1:272	55939	55939	+	panTro2.chrUn:307	9721935	9721935	+	canFam2.chr30:265	3361057	3361058	-
-10	canFam2.chr30:265_delete	1	hg18.chr1:272	55959	55959	+	panTro2.chrUn:307	9721955	9721955	+	canFam2.chr30:265	3361076	3361077	-
-10	canFam2.chr30:265_delete	3	hg18.chr1:272	56001	56003	+	panTro2.chrUn:307	9722032	9722034	+	canFam2.chr30:265	3361121	3361122	-
-12	canFam2.chr30:805_delete	6	hg18.chr1:802	56611	56616	+	panTro2.chrUn:801	9723790	9723795	+	canFam2.chr30:805	3359929	3359930	-
-12	canFam2.chr30:805_delete	1	hg18.chr1:802	56696	56696	+	panTro2.chrUn:801	9723875	9723875	+	canFam2.chr30:805	3360008	3360009	-
-12	canFam2.chr30:805_delete	7	hg18.chr1:802	56911	56917	+	panTro2.chrUn:801	9724090	9724096	+	canFam2.chr30:805	3360259	3360260	-
-12	canFam2.chr30:805_delete	3	hg18.chr1:802	56991	56993	+	panTro2.chrUn:801	9724170	9724172	+	canFam2.chr30:805	3360332	3360333	-
-12	canFam2.chr30:805_delete	5	hg18.chr1:802	57110	57114	+	panTro2.chrUn:801	9724289	9724293	+	canFam2.chr30:805	3360448	3360449	-
-12	canFam2.chr30:805_delete	1	hg18.chr1:802	57217	57217	+	panTro2.chrUn:801	9724395	9724395	+	canFam2.chr30:805	3360551	3360552	-
-12	canFam2.chr30:805_delete	5	hg18.chr1:802	57247	57251	+	panTro2.chrUn:801	9724425	9724429	+	canFam2.chr30:805	3360580	3360581	-
-12	canFam2.chr30:805_delete	2	hg18.chr1:802	57310	57311	+	panTro2.chrUn:801	9724488	9724489	+	canFam2.chr30:805	3360638	3360639	-
-12	canFam2.chr30:805_delete	2	hg18.chr1:802	57379	57380	+	panTro2.chrUn:801	9724557	9724558	+	canFam2.chr30:805	3360706	3360707	-
-12	canFam2.chr30:805_delete	4	hg18.chr1:802	57387	57390	+	panTro2.chrUn:801	9724565	9724568	+	canFam2.chr30:805	3360712	3360713	-
-13	canFam2.chr30:148_delete	3	hg18.chr1:176	58409	58411	+	panTro2.chrUn:176	9725587	9725589	+	canFam2.chr30:148	3359468	3359469	-
-13	canFam2.chr30:148_delete	1	hg18.chr1:176	58434	58434	+	panTro2.chrUn:176	9725612	9725612	+	canFam2.chr30:148	3359490	3359491	-
-13	canFam2.chr30:148_delete	2	hg18.chr1:176	58446	58447	+	panTro2.chrUn:176	9725624	9725625	+	canFam2.chr30:148	3359501	3359502	-
-13	canFam2.chr30:148_delete	8	hg18.chr1:176	58470	58477	+	panTro2.chrUn:176	9725648	9725655	+	canFam2.chr30:148	3359523	3359524	-
-13	canFam2.chr30:148_delete	5	hg18.chr1:176	58488	58492	+	panTro2.chrUn:176	9725666	9725670	+	canFam2.chr30:148	3359533	3359534	-
-13	canFam2.chr30:148_delete	6	hg18.chr1:176	58510	58515	+	panTro2.chrUn:176	9725688	9725693	+	canFam2.chr30:148	3359550	3359551	-
-13	canFam2.chr30:148_delete	5	hg18.chr1:176	58565	58569	+	panTro2.chrUn:176	9725743	9725747	+	canFam2.chr30:148	3359601	3359602	-
-14	canFam2.chr30:1623_delete	1	hg18.chr1:1628	58669	58669	+	panTro2.chrUn:1631	9725847	9725847	+	canFam2.chr30:1623	3356952	3356953	-
-14	canFam2.chr30:1623_delete	3	hg18.chr1:1628	58849	58851	+	panTro2.chrUn:1631	9726032	9726034	+	canFam2.chr30:1623	3357164	3357165	-
-14	canFam2.chr30:1623_delete	10	hg18.chr1:1628	59342	59351	+	panTro2.chrUn:1631	9726524	9726533	+	canFam2.chr30:1623	3357654	3357655	-
-14	canFam2.chr30:1623_delete	1	hg18.chr1:1628	59561	59561	+	panTro2.chrUn:1631	9726743	9726743	+	canFam2.chr30:1623	3357863	3357864	-
-14	canFam2.chr30:1623_delete	11	hg18.chr1:1628	59887	59897	+	panTro2.chrUn:1631	9727069	9727079	+	canFam2.chr30:1623	3358188	3358189	-
-14	canFam2.chr30:1623_delete	5	hg18.chr1:1628	59908	59912	+	panTro2.chrUn:1631	9727090	9727094	+	canFam2.chr30:1623	3358198	3358199	-
-14	canFam2.chr30:1623_delete	6	hg18.chr1:1628	60052	60057	+	panTro2.chrUn:1631	9727234	9727239	+	canFam2.chr30:1623	3358338	3358339	-
-14	canFam2.chr30:1623_delete	4	hg18.chr1:1628	60111	60114	+	panTro2.chrUn:1631	9727293	9727296	+	canFam2.chr30:1623	3358391	3358392	-
-14	canFam2.chr30:1623_delete	2	hg18.chr1:1628	60183	60184	+	panTro2.chrUn:1631	9727365	9727366	+	canFam2.chr30:1623	3358463	3358464	-
-15	canFam2.chr30:218_delete	4	hg18.chr1:230	60400	60403	+	panTro2.chrUn:230	9727581	9727584	+	canFam2.chr30:218	3356719	3356720	-
-15	canFam2.chr30:218_delete	8	hg18.chr1:230	60506	60513	+	panTro2.chrUn:230	9727687	9727694	+	canFam2.chr30:218	3356827	3356828	-
-15	canFam2.chr30:218_delete	10	hg18.chr1:230	60520	60529	+	panTro2.chrUn:230	9727701	9727710	+	canFam2.chr30:218	3356833	3356834	-
+#block	indel_type	indel_length	ingroup1	ingroup1_start	ingroup1_end	ingroup1_alignSize	ingroup1_orient	ingroup2	ingroup2_start	ingroup2_end	ingroup2_alignSize	ingroup2_orient	outgroup	outgroup_start	outgroup_end	outgroup_alignSize	outgroup_orient
+12	hg18.chr1_insert	1	hg18.chr1	57213	57213	802	+	panTro2.chrUn	9724391	9724392	801	+	canFam2.chr30	3360548	3360549	805	-
+2	hg18.chr1_delete	4	hg18.chr1	48103	48104	1380	+	panTro2.chrUn	9713713	9713716	1384	+	canFam2.chr30	3367755	3367758	1415	-
+9	hg18.chr1_delete	35	hg18.chr1	55389	55390	367	+	panTro2.chrUn	9721584	9721618	402	+	canFam2.chr30	3361661	3361695	382	-
+14	hg18.chr1_delete	1	hg18.chr1	58770	58771	1628	+	panTro2.chrUn	9725949	9725949	1631	+	canFam2.chr30	3357056	3357056	1623	-
+14	hg18.chr1_delete	4	hg18.chr1	58770	58771	1628	+	panTro2.chrUn	9725950	9725953	1631	+	canFam2.chr30	3357058	3357061	1623	-
+1	panTro2.chrUn_insert	2	hg18.chr1	46857	46858	143	+	panTro2.chrUn	9712465	9712466	145	+	canFam2.chr30	3368190	3368191	145	-
+8	panTro2.chrUn_insert	4	hg18.chr1	54744	54745	582	+	panTro2.chrUn	9720936	9720939	585	+	canFam2.chr30	3362635	3362636	600	-
+10	panTro2.chrUn_insert	35	hg18.chr1	55984	55985	272	+	panTro2.chrUn	9721981	9722015	307	+	canFam2.chr30	3361105	3361106	265	-
+8	panTro2.chrUn_delete	1	hg18.chr1	54979	54979	582	+	panTro2.chrUn	9721173	9721174	585	+	canFam2.chr30	3362890	3362890	600	-
+14	panTro2.chrUn_delete	1	hg18.chr1	59015	59015	1628	+	panTro2.chrUn	9726197	9726198	1631	+	canFam2.chr30	3357328	3357328	1623	-
+14	panTro2.chrUn_delete	1	hg18.chr1	60211	60211	1628	+	panTro2.chrUn	9727392	9727393	1631	+	canFam2.chr30	3358490	3358490	1623	-
+1	canFam2.chr30_insert	4	hg18.chr1	46796	46797	143	+	panTro2.chrUn	9712403	9712404	145	+	canFam2.chr30	3368127	3368130	145	-
+2	canFam2.chr30_insert	8	hg18.chr1	47138	47139	1380	+	panTro2.chrUn	9712747	9712748	1384	+	canFam2.chr30	3366730	3366737	1415	-
+2	canFam2.chr30_insert	3	hg18.chr1	47263	47264	1380	+	panTro2.chrUn	9712872	9712873	1384	+	canFam2.chr30	3366862	3366864	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	47293	47294	1380	+	panTro2.chrUn	9712902	9712903	1384	+	canFam2.chr30	3366895	3366895	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	47312	47313	1380	+	panTro2.chrUn	9712921	9712922	1384	+	canFam2.chr30	3366915	3366915	1415	-
+2	canFam2.chr30_insert	7	hg18.chr1	47440	47441	1380	+	panTro2.chrUn	9713049	9713050	1384	+	canFam2.chr30	3367044	3367050	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	47528	47529	1380	+	panTro2.chrUn	9713137	9713138	1384	+	canFam2.chr30	3367138	3367138	1415	-
+2	canFam2.chr30_insert	10	hg18.chr1	47546	47547	1380	+	panTro2.chrUn	9713155	9713156	1384	+	canFam2.chr30	3367157	3367166	1415	-
+2	canFam2.chr30_insert	4	hg18.chr1	47562	47563	1380	+	panTro2.chrUn	9713171	9713172	1384	+	canFam2.chr30	3367183	3367186	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	47648	47649	1380	+	panTro2.chrUn	9713257	9713258	1384	+	canFam2.chr30	3367273	3367273	1415	-
+2	canFam2.chr30_insert	3	hg18.chr1	47672	47673	1380	+	panTro2.chrUn	9713281	9713282	1384	+	canFam2.chr30	3367298	3367300	1415	-
+2	canFam2.chr30_insert	5	hg18.chr1	47734	47735	1380	+	panTro2.chrUn	9713343	9713344	1384	+	canFam2.chr30	3367361	3367365	1415	-
+2	canFam2.chr30_insert	2	hg18.chr1	47759	47760	1380	+	panTro2.chrUn	9713368	9713369	1384	+	canFam2.chr30	3367391	3367392	1415	-
+2	canFam2.chr30_insert	2	hg18.chr1	47835	47836	1380	+	panTro2.chrUn	9713444	9713445	1384	+	canFam2.chr30	3367469	3367470	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	48017	48018	1380	+	panTro2.chrUn	9713626	9713627	1384	+	canFam2.chr30	3367653	3367653	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	48035	48036	1380	+	panTro2.chrUn	9713644	9713645	1384	+	canFam2.chr30	3367672	3367672	1415	-
+2	canFam2.chr30_insert	4	hg18.chr1	48091	48092	1380	+	panTro2.chrUn	9713700	9713701	1384	+	canFam2.chr30	3367729	3367732	1415	-
+2	canFam2.chr30_insert	10	hg18.chr1	48103	48104	1380	+	panTro2.chrUn	9713712	9713713	1384	+	canFam2.chr30	3367745	3367754	1415	-
+2	canFam2.chr30_insert	1	hg18.chr1	48232	48233	1380	+	panTro2.chrUn	9713845	9713846	1384	+	canFam2.chr30	3367870	3367870	1415	-
+3	canFam2.chr30_insert	15	hg18.chr1	48379	48380	455	+	panTro2.chrUn	9714289	9714290	455	+	canFam2.chr30	3366038	3366052	483	-
+3	canFam2.chr30_insert	21	hg18.chr1	48426	48427	455	+	panTro2.chrUn	9714336	9714337	455	+	canFam2.chr30	3366096	3366116	483	-
+3	canFam2.chr30_insert	1	hg18.chr1	48523	48524	455	+	panTro2.chrUn	9714433	9714434	455	+	canFam2.chr30	3366213	3366213	483	-
+4	canFam2.chr30_insert	8	hg18.chr1	52535	52536	183	+	panTro2.chrUn	9718438	9718439	183	+	canFam2.chr30	3364655	3364662	193	-
+4	canFam2.chr30_insert	1	hg18.chr1	52555	52556	183	+	panTro2.chrUn	9718458	9718459	183	+	canFam2.chr30	3364683	3364683	193	-
+4	canFam2.chr30_insert	1	hg18.chr1	52588	52589	183	+	panTro2.chrUn	9718491	9718492	183	+	canFam2.chr30	3364717	3364717	193	-
+4	canFam2.chr30_insert	4	hg18.chr1	52691	52692	183	+	panTro2.chrUn	9718594	9718595	183	+	canFam2.chr30	3364817	3364820	193	-
+5	canFam2.chr30_insert	3	hg18.chr1	52709	52710	115	+	panTro2.chrUn	9718612	9718613	115	+	canFam2.chr30	3364525	3364527	118	-
+5	canFam2.chr30_insert	1	hg18.chr1	52754	52755	115	+	panTro2.chrUn	9718657	9718658	115	+	canFam2.chr30	3364571	3364571	118	-
+5	canFam2.chr30_insert	4	hg18.chr1	52763	52764	115	+	panTro2.chrUn	9718666	9718667	115	+	canFam2.chr30	3364581	3364584	118	-
+6	canFam2.chr30_insert	1	hg18.chr1	53848	53849	1040	+	panTro2.chrUn	9719751	9719752	1040	+	canFam2.chr30	3364511	3364511	1041	-
+7	canFam2.chr30_insert	4	hg18.chr1	53869	53870	335	+	panTro2.chrUn	9719772	9719773	335	+	canFam2.chr30	3363136	3363139	356	-
+7	canFam2.chr30_insert	1	hg18.chr1	53899	53900	335	+	panTro2.chrUn	9719802	9719803	335	+	canFam2.chr30	3363168	3363168	356	-
+7	canFam2.chr30_insert	1	hg18.chr1	53921	53922	335	+	panTro2.chrUn	9719824	9719825	335	+	canFam2.chr30	3363191	3363191	356	-
+7	canFam2.chr30_insert	8	hg18.chr1	53938	53939	335	+	panTro2.chrUn	9719841	9719842	335	+	canFam2.chr30	3363209	3363216	356	-
+7	canFam2.chr30_insert	7	hg18.chr1	53970	53971	335	+	panTro2.chrUn	9719873	9719874	335	+	canFam2.chr30	3363249	3363255	356	-
+7	canFam2.chr30_insert	5	hg18.chr1	54101	54102	335	+	panTro2.chrUn	9720004	9720005	335	+	canFam2.chr30	3363383	3363387	356	-
+7	canFam2.chr30_insert	1	hg18.chr1	54164	54165	335	+	panTro2.chrUn	9720067	9720068	335	+	canFam2.chr30	3363451	3363451	356	-
+8	canFam2.chr30_insert	1	hg18.chr1	54579	54580	582	+	panTro2.chrUn	9720770	9720771	585	+	canFam2.chr30	3362472	3362472	600	-
+8	canFam2.chr30_insert	1	hg18.chr1	54654	54655	582	+	panTro2.chrUn	9720845	9720846	585	+	canFam2.chr30	3362547	3362547	600	-
+8	canFam2.chr30_insert	1	hg18.chr1	54691	54692	582	+	panTro2.chrUn	9720882	9720883	585	+	canFam2.chr30	3362585	3362585	600	-
+8	canFam2.chr30_insert	18	hg18.chr1	54775	54776	582	+	panTro2.chrUn	9720970	9720971	585	+	canFam2.chr30	3362667	3362684	600	-
+8	canFam2.chr30_insert	1	hg18.chr1	54799	54800	582	+	panTro2.chrUn	9720994	9720995	585	+	canFam2.chr30	3362709	3362709	600	-
+8	canFam2.chr30_insert	4	hg18.chr1	54944	54945	582	+	panTro2.chrUn	9721139	9721140	585	+	canFam2.chr30	3362851	3362854	600	-
+8	canFam2.chr30_insert	1	hg18.chr1	54969	54970	582	+	panTro2.chrUn	9721164	9721165	585	+	canFam2.chr30	3362880	3362880	600	-
+9	canFam2.chr30_insert	1	hg18.chr1	55360	55361	367	+	panTro2.chrUn	9721554	9721555	402	+	canFam2.chr30	3361632	3361632	382	-
+9	canFam2.chr30_insert	1	hg18.chr1	55378	55379	367	+	panTro2.chrUn	9721572	9721573	402	+	canFam2.chr30	3361651	3361651	382	-
+9	canFam2.chr30_insert	1	hg18.chr1	55396	55397	367	+	panTro2.chrUn	9721625	9721626	402	+	canFam2.chr30	3361703	3361703	382	-
+9	canFam2.chr30_insert	2	hg18.chr1	55444	55445	367	+	panTro2.chrUn	9721673	9721674	402	+	canFam2.chr30	3361752	3361753	382	-
+10	canFam2.chr30_insert	1	hg18.chr1	55776	55777	272	+	panTro2.chrUn	9721772	9721773	307	+	canFam2.chr30	3360902	3360902	265	-
+10	canFam2.chr30_insert	5	hg18.chr1	55864	55865	272	+	panTro2.chrUn	9721860	9721861	307	+	canFam2.chr30	3360991	3360995	265	-
+10	canFam2.chr30_insert	2	hg18.chr1	55969	55970	272	+	panTro2.chrUn	9721965	9721966	307	+	canFam2.chr30	3361087	3361088	265	-
+10	canFam2.chr30_insert	2	hg18.chr1	55980	55981	272	+	panTro2.chrUn	9721976	9721977	307	+	canFam2.chr30	3361100	3361101	265	-
+12	canFam2.chr30_insert	33	hg18.chr1	56722	56723	802	+	panTro2.chrUn	9723901	9723902	801	+	canFam2.chr30	3360035	3360067	805	-
+12	canFam2.chr30_insert	1	hg18.chr1	56746	56747	802	+	panTro2.chrUn	9723925	9723926	801	+	canFam2.chr30	3360092	3360092	805	-
+12	canFam2.chr30_insert	1	hg18.chr1	56836	56837	802	+	panTro2.chrUn	9724015	9724016	801	+	canFam2.chr30	3360183	3360183	805	-
+12	canFam2.chr30_insert	1	hg18.chr1	56864	56865	802	+	panTro2.chrUn	9724043	9724044	801	+	canFam2.chr30	3360212	3360212	805	-
+12	canFam2.chr30_insert	1	hg18.chr1	56894	56895	802	+	panTro2.chrUn	9724073	9724074	801	+	canFam2.chr30	3360243	3360243	805	-
+12	canFam2.chr30_insert	2	hg18.chr1	57161	57162	802	+	panTro2.chrUn	9724340	9724341	801	+	canFam2.chr30	3360496	3360497	805	-
+12	canFam2.chr30_insert	1	hg18.chr1	57352	57353	802	+	panTro2.chrUn	9724530	9724531	801	+	canFam2.chr30	3360680	3360680	805	-
+13	canFam2.chr30_insert	2	hg18.chr1	58529	58530	176	+	panTro2.chrUn	9725707	9725708	176	+	canFam2.chr30	3359565	3359566	148	-
+14	canFam2.chr30_insert	1	hg18.chr1	58700	58701	1628	+	panTro2.chrUn	9725878	9725879	1631	+	canFam2.chr30	3356984	3356984	1623	-
+14	canFam2.chr30_insert	1	hg18.chr1	58709	58710	1628	+	panTro2.chrUn	9725887	9725888	1631	+	canFam2.chr30	3356994	3356994	1623	-
+14	canFam2.chr30_insert	1	hg18.chr1	58770	58771	1628	+	panTro2.chrUn	9725949	9725950	1631	+	canFam2.chr30	3357057	3357057	1623	-
+14	canFam2.chr30_insert	1	hg18.chr1	58772	58773	1628	+	panTro2.chrUn	9725955	9725956	1631	+	canFam2.chr30	3357064	3357064	1623	-
+14	canFam2.chr30_insert	15	hg18.chr1	58800	58801	1628	+	panTro2.chrUn	9725983	9725984	1631	+	canFam2.chr30	3357093	3357107	1623	-
+14	canFam2.chr30_insert	9	hg18.chr1	58808	58809	1628	+	panTro2.chrUn	9725991	9725992	1631	+	canFam2.chr30	3357116	3357124	1623	-
+14	canFam2.chr30_insert	1	hg18.chr1	60032	60033	1628	+	panTro2.chrUn	9727214	9727215	1631	+	canFam2.chr30	3358319	3358319	1623	-
+14	canFam2.chr30_insert	4	hg18.chr1	60148	60149	1628	+	panTro2.chrUn	9727330	9727331	1631	+	canFam2.chr30	3358426	3358429	1623	-
+15	canFam2.chr30_insert	1	hg18.chr1	60326	60327	230	+	panTro2.chrUn	9727507	9727508	230	+	canFam2.chr30	3356643	3356643	218	-
+15	canFam2.chr30_insert	2	hg18.chr1	60353	60354	230	+	panTro2.chrUn	9727534	9727535	230	+	canFam2.chr30	3356671	3356672	218	-
+15	canFam2.chr30_insert	1	hg18.chr1	60391	60392	230	+	panTro2.chrUn	9727572	9727573	230	+	canFam2.chr30	3356711	3356711	218	-
+15	canFam2.chr30_insert	1	hg18.chr1	60466	60467	230	+	panTro2.chrUn	9727647	9727648	230	+	canFam2.chr30	3356783	3356783	218	-
+15	canFam2.chr30_insert	5	hg18.chr1	60476	60477	230	+	panTro2.chrUn	9727657	9727658	230	+	canFam2.chr30	3356794	3356798	218	-
+1	canFam2.chr30_delete	1	hg18.chr1	46857	46857	143	+	panTro2.chrUn	9712464	9712464	145	+	canFam2.chr30	3368190	3368191	145	-
+1	canFam2.chr30_delete	1	hg18.chr1	46900	46900	143	+	panTro2.chrUn	9712509	9712509	145	+	canFam2.chr30	3368232	3368233	145	-
+2	canFam2.chr30_delete	7	hg18.chr1	47080	47086	1380	+	panTro2.chrUn	9712689	9712695	1384	+	canFam2.chr30	3366677	3366678	1415	-
+2	canFam2.chr30_delete	1	hg18.chr1	47168	47168	1380	+	panTro2.chrUn	9712777	9712777	1384	+	canFam2.chr30	3366766	3366767	1415	-
+2	canFam2.chr30_delete	1	hg18.chr1	47482	47482	1380	+	panTro2.chrUn	9713091	9713091	1384	+	canFam2.chr30	3367091	3367092	1415	-
+2	canFam2.chr30_delete	2	hg18.chr1	47703	47704	1380	+	panTro2.chrUn	9713312	9713313	1384	+	canFam2.chr30	3367330	3367331	1415	-
+2	canFam2.chr30_delete	15	hg18.chr1	48139	48153	1380	+	panTro2.chrUn	9713752	9713766	1384	+	canFam2.chr30	3367793	3367794	1415	-
+2	canFam2.chr30_delete	1	hg18.chr1	48160	48160	1380	+	panTro2.chrUn	9713773	9713773	1384	+	canFam2.chr30	3367799	3367800	1415	-
+2	canFam2.chr30_delete	1	hg18.chr1	48174	48174	1380	+	panTro2.chrUn	9713787	9713787	1384	+	canFam2.chr30	3367812	3367813	1415	-
+2	canFam2.chr30_delete	1	hg18.chr1	48197	48197	1380	+	panTro2.chrUn	9713810	9713810	1384	+	canFam2.chr30	3367834	3367835	1415	-
+2	canFam2.chr30_delete	5	hg18.chr1	48280	48284	1380	+	panTro2.chrUn	9713893	9713897	1384	+	canFam2.chr30	3367917	3367918	1415	-
+3	canFam2.chr30_delete	4	hg18.chr1	48344	48347	455	+	panTro2.chrUn	9714254	9714257	455	+	canFam2.chr30	3366005	3366006	483	-
+3	canFam2.chr30_delete	4	hg18.chr1	48410	48413	455	+	panTro2.chrUn	9714320	9714323	455	+	canFam2.chr30	3366082	3366083	483	-
+3	canFam2.chr30_delete	1	hg18.chr1	48470	48470	455	+	panTro2.chrUn	9714380	9714380	455	+	canFam2.chr30	3366159	3366160	483	-
+4	canFam2.chr30_delete	4	hg18.chr1	52639	52642	183	+	panTro2.chrUn	9718542	9718545	183	+	canFam2.chr30	3364767	3364768	193	-
+5	canFam2.chr30_delete	3	hg18.chr1	52707	52709	115	+	panTro2.chrUn	9718610	9718612	115	+	canFam2.chr30	3364524	3364525	118	-
+5	canFam2.chr30_delete	2	hg18.chr1	52743	52744	115	+	panTro2.chrUn	9718646	9718647	115	+	canFam2.chr30	3364560	3364561	118	-
+7	canFam2.chr30_delete	2	hg18.chr1	53879	53880	335	+	panTro2.chrUn	9719782	9719783	335	+	canFam2.chr30	3363148	3363149	356	-
+7	canFam2.chr30_delete	4	hg18.chr1	54052	54055	335	+	panTro2.chrUn	9719955	9719958	335	+	canFam2.chr30	3363336	3363337	356	-
+8	canFam2.chr30_delete	1	hg18.chr1	54634	54634	582	+	panTro2.chrUn	9720825	9720825	585	+	canFam2.chr30	3362526	3362527	600	-
+8	canFam2.chr30_delete	3	hg18.chr1	54710	54712	582	+	panTro2.chrUn	9720901	9720903	585	+	canFam2.chr30	3362603	3362604	600	-
+8	canFam2.chr30_delete	4	hg18.chr1	54876	54879	582	+	panTro2.chrUn	9721071	9721074	585	+	canFam2.chr30	3362785	3362786	600	-
+8	canFam2.chr30_delete	1	hg18.chr1	54984	54984	582	+	panTro2.chrUn	9721178	9721178	585	+	canFam2.chr30	3362894	3362895	600	-
+9	canFam2.chr30_delete	1	hg18.chr1	55131	55131	367	+	panTro2.chrUn	9721325	9721325	402	+	canFam2.chr30	3361420	3361421	382	-
+9	canFam2.chr30_delete	6	hg18.chr1	55213	55218	367	+	panTro2.chrUn	9721407	9721412	402	+	canFam2.chr30	3361501	3361502	382	-
+9	canFam2.chr30_delete	1	hg18.chr1	55308	55308	367	+	panTro2.chrUn	9721502	9721502	402	+	canFam2.chr30	3361590	3361591	382	-
+9	canFam2.chr30_delete	4	hg18.chr1	55324	55327	367	+	panTro2.chrUn	9721518	9721521	402	+	canFam2.chr30	3361605	3361606	382	-
+9	canFam2.chr30_delete	7	hg18.chr1	55340	55346	367	+	panTro2.chrUn	9721534	9721540	402	+	canFam2.chr30	3361617	3361618	382	-
+9	canFam2.chr30_delete	2	hg18.chr1	55386	55387	367	+	panTro2.chrUn	9721580	9721581	402	+	canFam2.chr30	3361658	3361659	382	-
+9	canFam2.chr30_delete	4	hg18.chr1	55457	55460	367	+	panTro2.chrUn	9721686	9721689	402	+	canFam2.chr30	3361765	3361766	382	-
+10	canFam2.chr30_delete	11	hg18.chr1	55893	55903	272	+	panTro2.chrUn	9721889	9721899	307	+	canFam2.chr30	3361023	3361024	265	-
+10	canFam2.chr30_delete	1	hg18.chr1	55924	55924	272	+	panTro2.chrUn	9721920	9721920	307	+	canFam2.chr30	3361043	3361044	265	-
+10	canFam2.chr30_delete	1	hg18.chr1	55939	55939	272	+	panTro2.chrUn	9721935	9721935	307	+	canFam2.chr30	3361057	3361058	265	-
+10	canFam2.chr30_delete	1	hg18.chr1	55959	55959	272	+	panTro2.chrUn	9721955	9721955	307	+	canFam2.chr30	3361076	3361077	265	-
+10	canFam2.chr30_delete	3	hg18.chr1	56001	56003	272	+	panTro2.chrUn	9722032	9722034	307	+	canFam2.chr30	3361121	3361122	265	-
+12	canFam2.chr30_delete	6	hg18.chr1	56611	56616	802	+	panTro2.chrUn	9723790	9723795	801	+	canFam2.chr30	3359929	3359930	805	-
+12	canFam2.chr30_delete	1	hg18.chr1	56696	56696	802	+	panTro2.chrUn	9723875	9723875	801	+	canFam2.chr30	3360008	3360009	805	-
+12	canFam2.chr30_delete	7	hg18.chr1	56911	56917	802	+	panTro2.chrUn	9724090	9724096	801	+	canFam2.chr30	3360259	3360260	805	-
+12	canFam2.chr30_delete	3	hg18.chr1	56991	56993	802	+	panTro2.chrUn	9724170	9724172	801	+	canFam2.chr30	3360332	3360333	805	-
+12	canFam2.chr30_delete	5	hg18.chr1	57110	57114	802	+	panTro2.chrUn	9724289	9724293	801	+	canFam2.chr30	3360448	3360449	805	-
+12	canFam2.chr30_delete	1	hg18.chr1	57217	57217	802	+	panTro2.chrUn	9724395	9724395	801	+	canFam2.chr30	3360551	3360552	805	-
+12	canFam2.chr30_delete	5	hg18.chr1	57247	57251	802	+	panTro2.chrUn	9724425	9724429	801	+	canFam2.chr30	3360580	3360581	805	-
+12	canFam2.chr30_delete	2	hg18.chr1	57310	57311	802	+	panTro2.chrUn	9724488	9724489	801	+	canFam2.chr30	3360638	3360639	805	-
+12	canFam2.chr30_delete	2	hg18.chr1	57379	57380	802	+	panTro2.chrUn	9724557	9724558	801	+	canFam2.chr30	3360706	3360707	805	-
+12	canFam2.chr30_delete	4	hg18.chr1	57387	57390	802	+	panTro2.chrUn	9724565	9724568	801	+	canFam2.chr30	3360712	3360713	805	-
+13	canFam2.chr30_delete	3	hg18.chr1	58409	58411	176	+	panTro2.chrUn	9725587	9725589	176	+	canFam2.chr30	3359468	3359469	148	-
+13	canFam2.chr30_delete	1	hg18.chr1	58434	58434	176	+	panTro2.chrUn	9725612	9725612	176	+	canFam2.chr30	3359490	3359491	148	-
+13	canFam2.chr30_delete	2	hg18.chr1	58446	58447	176	+	panTro2.chrUn	9725624	9725625	176	+	canFam2.chr30	3359501	3359502	148	-
+13	canFam2.chr30_delete	8	hg18.chr1	58470	58477	176	+	panTro2.chrUn	9725648	9725655	176	+	canFam2.chr30	3359523	3359524	148	-
+13	canFam2.chr30_delete	5	hg18.chr1	58488	58492	176	+	panTro2.chrUn	9725666	9725670	176	+	canFam2.chr30	3359533	3359534	148	-
+13	canFam2.chr30_delete	6	hg18.chr1	58510	58515	176	+	panTro2.chrUn	9725688	9725693	176	+	canFam2.chr30	3359550	3359551	148	-
+13	canFam2.chr30_delete	5	hg18.chr1	58565	58569	176	+	panTro2.chrUn	9725743	9725747	176	+	canFam2.chr30	3359601	3359602	148	-
+14	canFam2.chr30_delete	1	hg18.chr1	58669	58669	1628	+	panTro2.chrUn	9725847	9725847	1631	+	canFam2.chr30	3356952	3356953	1623	-
+14	canFam2.chr30_delete	3	hg18.chr1	58849	58851	1628	+	panTro2.chrUn	9726032	9726034	1631	+	canFam2.chr30	3357164	3357165	1623	-
+14	canFam2.chr30_delete	10	hg18.chr1	59342	59351	1628	+	panTro2.chrUn	9726524	9726533	1631	+	canFam2.chr30	3357654	3357655	1623	-
+14	canFam2.chr30_delete	1	hg18.chr1	59561	59561	1628	+	panTro2.chrUn	9726743	9726743	1631	+	canFam2.chr30	3357863	3357864	1623	-
+14	canFam2.chr30_delete	11	hg18.chr1	59887	59897	1628	+	panTro2.chrUn	9727069	9727079	1631	+	canFam2.chr30	3358188	3358189	1623	-
+14	canFam2.chr30_delete	5	hg18.chr1	59908	59912	1628	+	panTro2.chrUn	9727090	9727094	1631	+	canFam2.chr30	3358198	3358199	1623	-
+14	canFam2.chr30_delete	6	hg18.chr1	60052	60057	1628	+	panTro2.chrUn	9727234	9727239	1631	+	canFam2.chr30	3358338	3358339	1623	-
+14	canFam2.chr30_delete	4	hg18.chr1	60111	60114	1628	+	panTro2.chrUn	9727293	9727296	1631	+	canFam2.chr30	3358391	3358392	1623	-
+14	canFam2.chr30_delete	2	hg18.chr1	60183	60184	1628	+	panTro2.chrUn	9727365	9727366	1631	+	canFam2.chr30	3358463	3358464	1623	-
+15	canFam2.chr30_delete	4	hg18.chr1	60400	60403	230	+	panTro2.chrUn	9727581	9727584	230	+	canFam2.chr30	3356719	3356720	218	-
+15	canFam2.chr30_delete	8	hg18.chr1	60506	60513	230	+	panTro2.chrUn	9727687	9727694	230	+	canFam2.chr30	3356827	3356828	218	-
+15	canFam2.chr30_delete	10	hg18.chr1	60520	60529	230	+	panTro2.chrUn	9727701	9727710	230	+	canFam2.chr30	3356833	3356834	218	-
diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/getIndelRates_3way.py
--- a/tools/regVariation/getIndelRates_3way.py	Mon Sep 22 10:36:34 2008 -0400
+++ b/tools/regVariation/getIndelRates_3way.py	Mon Sep 22 12:02:35 2008 -0400
@@ -1,56 +1,56 @@
 #!/usr/bin/env python
 #Guruprasad Ananda
 
-import sys, os, tempfile, string
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
 
-assert sys.version_info[:2] >= ( 2, 4 )
+import sys, os, tempfile
+import traceback
+import fileinput
+from warnings import warn
 
-fout = open(sys.argv[2],'w')
-winsize = int(sys.argv[3])
-species_ind = int(sys.argv[4]) 
+from galaxy.tools.util.galaxyops import *
+from bx.intervals.io import *
+
+from bx.intervals.operations import quicksect
 
 def stop_err(msg):
     sys.stderr.write(msg)
     sys.exit()
+    
+def counter(node, start, end, sort_col):
+    global full, blk_len, blk_list
+    if node.start < start:
+        if node.right:
+            counter(node.right, start, end, sort_col)
+    elif start <= node.start <= end and start <= node.end <= end:
+        full += 1
+        if node.other[0] not in blk_list:
+            blk_list.append(node.other[0])
+            blk_len += int(node.other[sort_col+2])
+        if node.left and node.left.maxend > start:
+            counter(node.left, start, end, sort_col)
+        if node.right: 
+            counter(node.right, start, end, sort_col)
+    elif node.start > end:
+        if node.left: 
+            counter(node.left, start, end, sort_col)
+            
 
-def rate_estimator(win, blk_lines, wstart, wend, wspecies):
-    inserts = 0.0
-    deletes = 0.0
-    ilengths = {}    #dict containing lengths of blocks(without gaps) having insertion in wspecies
-    dlengths = {}    #dict containing lengths of blocks(without gaps) having deletion in wspecies
-    prev_bnum = -1
-    for bline in blk_lines:
-        items = bline.split('\t')
-        bnum = int(items[0])
-        bevent = items[1]
-        if not(bevent.startswith(wspecies)):
-            continue
-        if bevent.endswith('insert'):
-            inserts += 1
-            #Add lengths only if the insert belongs to a new alignment block
-            if not(ilengths.has_key(bnum)):
-                ilengths[bnum] = int(items[species_ind].split(':')[1])
-                #prev_bnum = bnum
-        elif bevent.endswith('delete'):
-            deletes += 1
-            #Add lengths only if the delete belongs to a new alignment block
-            if not(dlengths.has_key(bnum)):
-                dlengths[bnum] = int(items[species_ind].split(':')[1])
-                #prev_bnum = bnum
+infile = sys.argv[1]  
+fout = open(sys.argv[2],'w')
+int_file = sys.argv[3]
+if int_file != "None": #User has specified an interval file
     try:
-        total_ilength = sum(ilengths.values())
-        irate = inserts/total_ilength
+        fint = open(int_file, 'r')
+        dbkey_i = sys.argv[4]
+        chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[5] )
     except:
-        irate = 0
-    try:
-        total_dlength = sum(dlengths.values())
-        drate = deletes/total_dlength
-    except:
-        drate = 0
-    print >>fout, "%s\t%s\t%s\t%s\t%.2e\t%.2e" %(win, wspecies, wstart, wend, irate , drate)
-    
+        stop_err("Unable to open input Interval file")
+        
 def main():
-    infile = sys.argv[1]
+
     for i, line in enumerate( file ( infile )):
         line = line.rstrip('\r\n')
         if len( line )>0 and not line.startswith( '#' ):
@@ -58,71 +58,192 @@
             break
         if i == 30:
             break # Hopefully we'll never get here...
-    
-    if len( elems ) != 15:
+        
+    if len( elems ) != 18:
         stop_err( "This tool only works on tabular data output by 'Fetch Indels from 3-way alignments' tool. The data in your input dataset is either missing or not formatted properly." )
     
-    wspecies = elems[species_ind].split(':')[0].split('.')[0]
-    fin = open(infile, 'r')
-    skipped = 0
-    blk=0
-    win=0
-    linestr=""
-    sorted_infile = tempfile.NamedTemporaryFile()
-    cmdline = "sort -n -k"+str(species_ind+2)+" -o "+sorted_infile.name+" "+infile
-    try:
-        os.system(cmdline)
-    except:
-        stop_err("Encountered error while sorting the input file.")
-    
-    print >>fout, "#Window\tSpecies\tWindow_Start\tWindow_End\tInsertion_Rate\tDeletion_Rate"
-    
-    for line in sorted_infile.readlines():
-        line = line.strip("\r\n")
-        if not(line) or line == "":
-            continue
+    for i, line in enumerate( file ( infile )):
+        line = line.rstrip('\r\n')
         elems = line.split('\t')
         try:
             assert int(elems[0])
-            assert len(elems) == 15
-        except Exception, eon:
+            assert len(elems) == 18
+            if int_file != "None":
+                if dbkey_i not in elems[3] and  dbkey_i not in elems[8] and dbkey_i not in elems[13]:
+                    stop_err("The species build corresponding to your interval file is not present in the Indel file.") 
+                if dbkey_i in elems[3]:
+                    sort_col = 4
+                elif dbkey_i in elems[8]:
+                    sort_col = 9
+                elif dbkey_i in elems[13]:
+                    sort_col = 14
+            else:
+                species = []
+                species.append( elems[3].split('.')[0] )
+                species.append( elems[8].split('.')[0] )
+                species.append( elems[13].split('.')[0] )
+                sort_col = 0    #Based on block numbers
+            break
+        except:
             continue
         
-        if not(elems[1].startswith(wspecies)):    #Event doesn't belong to the selected species
+        
+    fin = open(infile, 'r')
+    skipped = 0
+    
+    if int_file == "None":
+        sorted_infile = tempfile.NamedTemporaryFile()
+        cmdline = "sort -n -k"+str(1)+" -o "+sorted_infile.name+" "+infile
+        try:
+            os.system(cmdline)
+        except:
+            stop_err("Encountered error while sorting the input file.")
+        print >>fout, "#Block\t%s_InsRate\t%s_InsRate\t%s_InsRate\t%s_DelRate\t%s_DelRate\t%s_DelRate" %(species[0],species[1],species[2],species[0],species[1],species[2])
+        prev_bnum = -1
+        sorted_infile.seek(0)
+        for line in sorted_infile.readlines():
+            line = line.rstrip('\r\n')
+            elems = line.split('\t')
+            try:
+                assert int(elems[0])
+                assert len(elems) == 18
+                new_bnum = int(elems[0])
+                if new_bnum != prev_bnum:
+                    if prev_bnum != -1:
+                        irate = []
+                        drate = []
+                        for i,elem in enumerate(inserts):
+                            try:
+                                irate.append(str("%.2e" %(inserts[i]/blen[i])))
+                            except:
+                                irate.append('0')
+                            try:
+                                drate.append(str("%.2e" %(deletes[i]/blen[i])))
+                            except:
+                                drate.append('0')
+                        print >>fout, "%s\t%s\t%s" %(prev_bnum, '\t'.join(irate) , '\t'.join(drate))
+                    inserts = [0.0, 0.0, 0.0]
+                    deletes = [0.0, 0.0, 0.0]
+                    blen = []
+                    blen.append( int(elems[6]) )
+                    blen.append( int(elems[11]) )
+                    blen.append( int(elems[16]) )
+                line_sp = elems[1].split('.')[0]
+                sp_ind = species.index(line_sp)
+                if elems[1].endswith('insert'):
+                    inserts[sp_ind] += 1
+                elif elems[1].endswith('delete'):
+                    deletes[sp_ind] += 1
+                prev_bnum = new_bnum 
+            except Exception, ei:
+                #print >>sys.stderr, ei
+                continue
+        irate = []
+        drate = []
+        for i,elem in enumerate(inserts):
+            try:
+                irate.append(str("%.2e" %(inserts[i]/blen[i])))
+            except:
+                irate.append('0')
+            try:
+                drate.append(str("%.2e" %(deletes[i]/blen[i])))
+            except:
+                drate.append('0')
+        print >>fout, "%s\t%s\t%s" %(prev_bnum, '\t'.join(irate) , '\t'.join(drate))
+        sys.exit()
+    
+    
+    inf = open(infile, 'r')
+    start_met = False
+    end_met = False
+    sp_file = tempfile.NamedTemporaryFile()
+    for n, line in enumerate(inf):
+        line = line.rstrip('\r\n')
+        elems = line.split('\t')
+        try:
+            assert int(elems[0])
+            assert len(elems) == 18
+            if dbkey_i not in elems[1]: 
+                if not(start_met):   
+                    continue
+                else:
+                    sp_end = n
+                    break
+            else:
+                print >>sp_file, line
+                if not(start_met):
+                    start_met = True
+                    sp_start = n
+        except:
             continue
-        
-        try:
-            assert wstart
-        except NameError:
-            wstart = int(elems[species_ind+1]) - int(elems[species_ind+1])%winsize + 1
-            wend = wstart + winsize
-        lstart = int(elems[species_ind + 1])
-        
-        if lstart in range(wstart,wend+1):
-            linestr += line.strip()
-            linestr += "\n"
-        else:
-            try:
-                win += 1
-                blk_lines = linestr.strip().split("\n")
-                rate_estimator(str(win), blk_lines, str(wstart), str(wend), wspecies)
-                linestr = ""
-            except:
-                skipped += 1
-                pass
-            linestr=line.strip()+"\n"
-            wstart = int(elems[species_ind+1]) - int(elems[species_ind+1])%winsize + 1
-            wend = wstart + winsize
-    if linestr != "":
-        try:
-            win += 1
-            blk_lines = linestr.strip().split("\n")
-            rate_estimator(str(win), blk_lines, str(wstart), str(wend), wspecies)
-        except:
-            skipped += 1
+    
+    try:
+        assert sp_end
+    except:
+        sp_end = n+1
+    
+    sp_file.seek(0)
+    win = NiceReaderWrapper( fileinput.FileInput( int_file ),
+                                chrom_col=chr_col_i,
+                                start_col=start_col_i,
+                                end_col=end_col_i,
+                                strand_col=strand_col_i,
+                                fix_strand=True)
+    
+    indel = NiceReaderWrapper( fileinput.FileInput( sp_file.name ),
+                                chrom_col=1,
+                                start_col=sort_col,
+                                end_col=sort_col+1,
+                                strand_col=-1,
+                                fix_strand=True)
+    
+    indelTree = quicksect.IntervalTree()
+    for item in indel:
+        if type( item ) is GenomicInterval:
+            indelTree.insert( item, indel.linenum, item.fields )
+    result=[]
+    
+    global full, blk_len, blk_list
+    for interval in win:
+        if type( interval ) is Header:
             pass
-    if skipped:
-        print "Skipped %s windows as invalid." %(skipped)
+        if type( interval ) is Comment:
+            pass
+        elif type( interval ) == GenomicInterval:
+            chrom = interval.chrom
+            start = int(interval.start)
+            end = int(interval.end)
+            if start > end: 
+                warn( "Interval start after end!" )
+            ins_chr = "%s.%s_insert" %(dbkey_i,chrom)
+            del_chr = "%s.%s_delete" %(dbkey_i,chrom)
+            irate = 0
+            drate = 0
+            if ins_chr not in indelTree.chroms and del_chr not in indelTree.chroms:
+                pass    
+            else:
+                if ins_chr in indelTree.chroms:
+                    full = 0.0
+                    blk_len = 0
+                    blk_list = []
+                    root = indelTree.chroms[ins_chr]    #root node for the chrom insertion tree
+                    counter(root, start, end, sort_col)
+                    if blk_len:
+                        irate = full/blk_len
+                
+                if del_chr in indelTree.chroms:
+                    full = 0.0
+                    blk_len = 0
+                    blk_list = []
+                    root = indelTree.chroms[del_chr]    #root node for the chrom insertion tree
+                    counter(root, start, end, sort_col)
+                    if blk_len:
+                        drate = full/blk_len
+                
+            interval.fields.append(str("%.2e" %irate))
+            interval.fields.append(str("%.2e" %drate))
+            print >>fout, "\t".join(interval.fields)
+            fout.flush()
+
 if __name__ == "__main__":
-    main()
-    
\ No newline at end of file
+    main()    
\ No newline at end of file
diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/getIndelRates_3way.xml
--- a/tools/regVariation/getIndelRates_3way.xml	Mon Sep 22 10:36:34 2008 -0400
+++ b/tools/regVariation/getIndelRates_3way.xml	Mon Sep 22 12:02:35 2008 -0400
@@ -1,30 +1,30 @@
-<tool id="getIndelRates_3way" name="Estimate Indel Rates" version="1.0.0">
+<tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.0">
   <description> for 3-way alignments</description>
   <command interpreter="python">
-  	getIndelRates_3way.py $input1 $out_file1 $winsize $species
+    getIndelRates_3way.py $input1 $out_file1 
+    #if $region.type == "align"
+        "None"
+    #else
+        $region.input2 $input2_dbkey $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol
+    #end if
   </command>
   <inputs>
     <page>
-    	<param format="tabular" name="input1" type="data" label="Select data"/>
-    	<param name="winsize" size="10" type="integer" value="1000" label="Estimate rates in windows of size" />
-    	<param name="species" type="select" label="and corresponding to co-ordinates of" multiple="false">
-          <option value="3">Species 1 (Ingroup 1)</option>
-          <option value="7">Species 2 (Ingroup 2)</option>
-          <option value="11">Species 3 (Outgroup)</option>
-        </param>
-    	<!--
-    	<conditional name="region">
-	      <param name="type" type="select" label="Estimate rates per" multiple="false">
-	         <option value="align">Alignment block</option>
-	         <option value="win">Window</option>
-	     </param>
-	     <when value="win">
-	      	<param name="winsize" size="10" type="integer" value="1000" label="of size" />
-
-	      </when>
-	      <when value="align" />
+        <param format="tabular" name="input1" type="data" label="Select dataset containing Indels"/>
+        
+        <conditional name="region">
+          <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
+            <option value="align" selected="True">Alignment block</option>
+            <option value="win">Intervals in your history</option>
+         </param>
+         <when value="win">
+            <param format="interval" name="input2" type="data" label="Choose intervals">
+                <validator type="unspecified_build" />
+            </param>
+          </when>
+          <when value="align" />
       </conditional>
-      -->
+     
     </page>
   </inputs>
   <outputs>
@@ -34,8 +34,7 @@
   <tests>
     <test>
       <param name="input1" value="indels_3way.tabular"/>
-      <param name="winsize" value="1000"/>
-      <param name="species" value="11"/>
+      <param name="type" value="align"/>
       <output name="out_file1" file="indelrates_3way.tabular"/>
     </test>
   </tests>
@@ -54,8 +53,8 @@
 
 **Note**
 
-Any block/s not containing exactly 3 species will be omitted. 
-   
+This tool only works on the output of the 'Estimate Indel Rates for 3-way alignments' tool.   
+
 </help>  
 
 
diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/getIndels_3way.xml
--- a/tools/regVariation/getIndels_3way.xml	Mon Sep 22 10:36:34 2008 -0400
+++ b/tools/regVariation/getIndels_3way.xml	Mon Sep 22 12:02:35 2008 -0400
@@ -1,4 +1,4 @@
-<tool id="getIndels_3way" name="Fetch Indels"  version="1.0.1">
+<tool id="indels_3way" name="Fetch Indels"  version="1.0.1">
   <description> from 3-way alignments</description>
   <command interpreter="perl">
   	parseMAF_smallIndels.pl $input1 $out_file1 $outgroup
diff -r aae4754d6828 -r 675ad84ae008 tools/regVariation/parseMAF_smallIndels.pl
--- a/tools/regVariation/parseMAF_smallIndels.pl	Mon Sep 22 10:36:34 2008 -0400
+++ b/tools/regVariation/parseMAF_smallIndels.pl	Mon Sep 22 12:02:35 2008 -0400
@@ -58,7 +58,7 @@
 #print OFILE "#align\tingroup1\tingroup1_coord\tingroup1_orient\tingroup2\tingroup2_coord\tingroup2_orient\toutgroup\toutgroup_coord\toutgroup_orient\tindel_type\n";
 
 #print OFILE2 "# small indels summary, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n";
-print OFILE2 "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_orient\n";
+print OFILE2 "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_alignSize\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_alignSize\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_alignSize\toutgroup_orient\n";
 
 # main body of program
 while ($record = get_next_record($fh) ){
@@ -348,7 +348,8 @@
 		    		&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
 	       			&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
 					$ABC = join("",($ABC,"X"));
-					$indelType = $seq1."_delete";
+					my @s = split(/:/, $seq1);
+					$indelType = $s[0]."_delete";
 
 					#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";	
 					$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
@@ -361,7 +362,8 @@
 				&& (substr($sequence2,$position,1) eq "-")
 				&& (substr($sequence3,$position,1) !~ m/[-*\$?^]/)){
 					$ABC = join("",($ABC,"Y"));
-					$indelType = $seq2."_delete";
+					my @s = split(/:/, $seq2);
+					$indelType = $s[0]."_delete";
 					#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
 					$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
                                         push (@indels,$indel_line);
@@ -375,7 +377,8 @@
 				&& (substr($sequence2,$position,1) eq "-")
 				&& (substr($sequence3,$position,1) eq "-")){
 					$ABC = join("",($ABC,"Z"));
-					$indelType = $seq1."_insert";
+					my @s = split(/:/, $seq1);
+					$indelType = $s[0]."_insert";
 					#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
 					$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
 					push (@indels,$indel_line);
@@ -387,7 +390,8 @@
 				&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
 				&& (substr($sequence3,$position,1) eq "-")){
 					$ABC = join("",($ABC,"W"));
-					$indelType = $seq2."_insert";
+					my @s = split(/:/, $seq2);
+					$indelType = $s[0]."_insert";
 					#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
 					$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
 					push (@indels,$indel_line);
@@ -399,7 +403,8 @@
 				&& (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/)
 				&& (substr($sequence3,$position,1) eq "-")){
 					$ABC = join("",($ABC,"S"));
-					$indelType = $seq3."_delete";
+					my @s = split(/:/, $seq3);
+					$indelType = $s[0]."_delete";
 					#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
 					$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
 					push (@indels,$indel_line);
@@ -411,7 +416,8 @@
 				&& (substr($sequence2,$position,1) eq "-")
 				&& (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){
 					$ABC = join("",($ABC,"T"));
-					$indelType = $seq3."_insert";
+					my @s = split(/:/, $seq3);
+					$indelType = $s[0]."_insert";
 					#print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n";
 					$indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType));
 					push (@indels,$indel_line);
@@ -622,6 +628,9 @@
 		my $event_line = $_;
 		my @events = split(/\t/, $event_line);
 		my $event_type = $events[10];
+		my @name_align1 = split(/:/, $events[1]);
+		my @name_align2 = split(/:/, $events[4]);
+		my @name_align3 = split(/:/, $events[7]);
 		my $seq1_event_start = my $seq1_event_end = my $seq2_event_start = my $seq2_event_end = my $seq3_event_start = my $seq3_event_end = 0;
 		my $final_event_line = "";	
 		# seq1_insert
@@ -634,7 +643,7 @@
 			$seq2_event_end = ($events[5]);
 			$seq3_event_start = ($events[8]-1);
 			$seq3_event_end = ($events[8]);
-			$final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9]));
+			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
 		}
 		# seq1_delete
 		elsif ($event_type =~ m/$ingroup1/ && $event_type =~ m/delete/){
@@ -646,7 +655,7 @@
                         $seq2_event_end = ($events[5]+$events[11]-1);
                         $seq3_event_start = ($events[8]);
                         $seq3_event_end = ($events[8]+$events[11]-1);
-			$final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9]));
+			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
 		}
 		# seq2_insert
 		elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/insert/){	
@@ -658,7 +667,7 @@
                         $seq2_event_end = ($events[5]+$events[11]-1);
                         $seq3_event_start = ($events[8]-1);
 			$seq3_event_end = ($events[8]);			
-			$final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9]));
+			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
 		}
 		# seq2_delete
 		elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/delete/){
@@ -670,7 +679,7 @@
 	                $seq2_event_end = ($events[5]);
                         $seq3_event_start = ($events[8]);
                         $seq3_event_end = ($events[8]+$events[11]-1);
-			$final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9]));
+			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
 		}	
 		# start testing w/seq3_insert
 		elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/insert/){
@@ -682,7 +691,7 @@
 			$seq2_event_end = ($events[5]);
 			$seq3_event_start = ($events[8]);
 			$seq3_event_end = ($events[8]+$events[11]-1);
-			$final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9]));
+			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
 		}
 		# seq3_delete
 		elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/delete/){
@@ -694,7 +703,7 @@
 			$seq2_event_end = ($events[5]+$events[11]-1);
 			$seq3_event_start = ($events[8]-1);
 			$seq3_event_end = ($events[8]);
-			$final_event_line = join("\t",($events[0],$event_type,$events[11],$events[1],$seq1_event_start,$seq1_event_end,$events[3],$events[4],$seq2_event_start,$seq2_event_end,$events[6],$events[7],$seq3_event_start,$seq3_event_end,$events[9]));
+			$final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9]));
 
 		}

    

[galaxy-dev] [hg] galaxy 1525: Modified INDEL tools under Regional variation ...

greg＠scofield.bx.psu.edu