# HG changeset patch
# User mvdbeek
# Date 1446221300 14400
# Node ID eace1635959aa9a6c6e3c3386fbea4075602c675
# Parent  71db297a0edd426327426c0d78e2040aef93e721
planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty

diff -r 71db297a0edd -r eace1635959a dapars.py
--- a/dapars.py	Fri Oct 30 11:54:18 2015 -0400
+++ b/dapars.py	Fri Oct 30 12:08:20 2015 -0400
@@ -365,7 +365,8 @@
     get minima for numpy array a. If local is false, only return absolute minimum
     """
     if not local_minimum:
-        return np.where(a == a.min())
+        print np.where(a == a.min())[0]
+        return np.where(a == a.min())[0]
     else:
         return np.where(np.r_[True, a[1:] < a[:-1]] & np.r_[a[:-1] < a[1:], True])[0]+1
 
diff -r 71db297a0edd -r eace1635959a filter_utr.pyc
Binary file filter_utr.pyc has changed
diff -r 71db297a0edd -r eace1635959a test-data/breakpoint.bed
--- a/test-data/breakpoint.bed	Fri Oct 30 11:54:18 2015 -0400
+++ b/test-data/breakpoint.bed	Fri Oct 30 12:08:20 2015 -0400
@@ -1,3 +1,2 @@
-3L	3371372	3371373	FBgn0027616_control_breakpoint	0	-
-3L	3370784	3370785	FBgn0027616_control_breakpoint	0	-
-3L	3371377	3371378	FBgn0027616_treatment_breakpoint	0	-
+3L	[3371373]	3371374	FBgn0027616_control_breakpoint	0	-
+3L	[3371378]	3371379	FBgn0027616_treatment_breakpoint	0	-
diff -r 71db297a0edd -r eace1635959a test-data/dapars.tab
--- a/test-data/dapars.tab	Fri Oct 30 11:54:18 2015 -0400
+++ b/test-data/dapars.tab	Fri Oct 30 12:08:20 2015 -0400
@@ -1,4 +1,3 @@
-#chr	start	end	strand	gene	t_stat	p_value	breakpoint	breakpoint_type	control_mean_percent	treatment_mean_percent	control_0_coverage_long	control_1_coverage_long	control_2_coverage_long	treatment_0_coverage_long	treatment_1_coverage_long	treatment_2_coverage_long	control_0_coverage_short	control_1_coverage_short	control_2_coverage_short	treatment_0_coverage_short	treatment_1_coverage_short	treatment_2_coverage_short	control_0_percent_long	control_1_percent_long	control_2_percent_long	treatment_0_percent_long	treatment_1_percent_long	treatment_2_percent_long
-3L	3370451	3371600	-	FBgn0027616	9.1011438605826918	0.00080834574079269837	3371372	control_breakpoint	0.28613352633890804	0.1552722208119959	123.62701047322379	125.76921390717855	124.10039158598833	75.98660341468468	74.9663604415773	92.02422062460907	313.2767927742506	306.7750174396159	311.8400395723512	457.86960717999216	460.96613409837073	409.1940321393445	0.28296162577279749	0.290766133940976	0.28467281930295052	0.1423353365694503	0.13988022970305145	0.18360109616348599
-3L	3370451	3371600	-	FBgn0027616	7.6359778766491502	0.0015797924799674865	3370784	control_breakpoint	0.43563602087116343	0.30952531200299072	126.49368847128825	135.6040569502353	143.91168970217444	78.65135923183745	75.39920267528716	91.12897666960338	176.25202990071813	175.09090450634255	174.0320885673699	182.34958166653055	182.76407220805163	180.75929709112899	0.41782156045508784	0.4364539943438609	0.45263250781454173	0.30134511761190835	0.29206014182055623	0.33517067657650756
-3L	3370451	3371600	-	FBgn0027616	9.1454409776006926	0.00079338758637485167	3371377	treatment_breakpoint	0.28605861729684262	0.15575482035230456	124.36386257923384	126.4043948424219	124.8955647308763	77.16902750245079	76.14856990419119	93.05673684054834	315.2259541806009	308.84814706202656	313.5640869173955	462.7362682995148	465.9257702994563	413.0782709512907	0.28290887968221229	0.29041621282517777	0.28485075938313781	0.14293067340231458	0.14047624883993506	0.18385753881466405
+#chr	start	end	strand	gene	t_stat	p_value	adj_p_value	breakpoint	breakpoint_type	control_mean_percent	treatment_mean_percent	control_0_coverage_long	control_1_coverage_long	control_2_coverage_long	treatment_0_coverage_long	treatment_1_coverage_long	treatment_2_coverage_long	control_0_coverage_short	control_1_coverage_short	control_2_coverage_short	treatment_0_coverage_short	treatment_1_coverage_short	treatment_2_coverage_short	control_0_percent_long	control_1_percent_long	control_2_percent_long	treatment_0_percent_long	treatment_1_percent_long	treatment_2_percent_long
+3L	3370451	3371600	-	FBgn0027616	9.1054958679604052	0.00080686075938347099	0.00080686075938347099	[3371373]	control_breakpoint	0.28606762973007355	0.15530974331433603	123.76469554964986	125.88195883295893	124.23928385838184	76.197448636884261	75.16883097093779	92.213645811041374	313.69192063476942	307.22820497250859	312.24306733982991	458.90822949180267	462.0484587539213	410.0129667530764	0.28291878776265711	0.29064651294929922	0.28463758847826431	0.14239701006977473	0.13992258329853127	0.18360963657470208
+3L	3370451	3371600	-	FBgn0027616	9.1549876337742582	0.00079020897804143021	0.00080686075938347099	[3371378]	treatment_breakpoint	0.28605900858035477	0.15586977387982176	124.51650401545287	126.53562209286154	125.06102209271751	77.416443129523003	76.396087272687623	93.271359050104479	315.60576665411662	309.25736837469651	313.89372333010442	463.69514727744564	466.90329316965784	413.84500622985172	0.28291343636399646	0.29035717613792433	0.28490641323914345	0.14306927536203448	0.1406150826280847	0.18392496364934613