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

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

greg
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]));
 
  }