Mercurial > repos > mvdbeek > dapars
changeset 21:eace1635959a draft
planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 30 Oct 2015 12:08:20 -0400 |
| parents | 71db297a0edd |
| children | 4309798bfb61 |
| files | dapars.py filter_utr.pyc test-data/breakpoint.bed test-data/dapars.tab |
| diffstat | 4 files changed, 7 insertions(+), 8 deletions(-) [+] |
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--- 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
--- 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 -
--- 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