Mercurial > repos > mvdbeek > dapars
changeset 14:ea5d573d6d40 draft
planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 30 Oct 2015 06:58:57 -0400 |
| parents | 538c4e2b423e |
| children | 8af6d4ad2f0a |
| files | dapars.py filter_utr.pyc test-data/breakpoint.bed test-data/dapars.tab |
| diffstat | 4 files changed, 11 insertions(+), 28 deletions(-) [+] |
line wrap: on
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--- a/dapars.py Fri Oct 30 04:59:15 2015 -0400 +++ b/dapars.py Fri Oct 30 06:58:57 2015 -0400 @@ -256,8 +256,8 @@ res["treatment_{i}_coverage_short".format(i=k)] = float(short_coverage_vector[i]) res["treatment_{i}_percent_long".format(i=k)] = percentage_long[i] res["t_stat"], res["p_value"] = stat_test(percentage_long[:num_control], percentage_long[num_control:]) - control_mean_percent = np.mean(np.array(percentage_long[:num_control])) - treatment_mean_percent = np.mean(np.array(percentage_long[num_control:])) + control_mean_percent = np.mean(percentage_long[:num_control]) + treatment_mean_percent = np.mean(percentage_long[num_control:]) res["chr"] = utr_d["chr"] res["start"] = utr_d["start"] res["end"] = utr_d["end"] @@ -380,7 +380,8 @@ return stats.ttest_ind(a,b) def gene_str_to_link(str): - return "<a href=\"{str}.svg\" type=\"image/svg+xml\" target=\"_blank\">{str}</a>".format(str=str) + return "<a href=\"{str}.svg\" type=\"image/svg+xml\">{str}</a>".format(str=str) + if __name__ == '__main__': args = parse_args()
--- a/test-data/breakpoint.bed Fri Oct 30 04:59:15 2015 -0400 +++ b/test-data/breakpoint.bed Fri Oct 30 06:58:57 2015 -0400 @@ -1,12 +1,3 @@ -3L 3371595 3371596 FBgn0027616_control_breakpoint 0 - -3L 3371497 3371498 FBgn0027616_control_breakpoint 0 - -3L 3371403 3371404 FBgn0027616_control_breakpoint 0 - -3L 3371303 3371304 FBgn0027616_control_breakpoint 0 - -3L 3371189 3371190 FBgn0027616_control_breakpoint 0 - -3L 3370936 3370937 FBgn0027616_control_breakpoint 0 - -3L 3371400 3371401 FBgn0027616_treatment_breakpoint 0 - -3L 3371361 3371362 FBgn0027616_treatment_breakpoint 0 - -3L 3371337 3371338 FBgn0027616_treatment_breakpoint 0 - -3L 3371318 3371319 FBgn0027616_treatment_breakpoint 0 - -3L 3371310 3371311 FBgn0027616_treatment_breakpoint 0 - -3L 3371195 3371196 FBgn0027616_treatment_breakpoint 0 - +3L 3371372 3371373 FBgn0027616_control_breakpoint 0 - +3L 3370784 3370785 FBgn0027616_control_breakpoint 0 - +3L 3371377 3371378 FBgn0027616_treatment_breakpoint 0 -
--- a/test-data/dapars.tab Fri Oct 30 04:59:15 2015 -0400 +++ b/test-data/dapars.tab Fri Oct 30 06:58:57 2015 -0400 @@ -1,13 +1,4 @@ -#chr start end strand gene 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 control_0_coverage_short control_1_coverage_short control_2_coverage_short treatment_0_coverage_short treatment_1_coverage_short control_0_percent_long control_1_percent_long control_2_percent_long treatment_0_percent_long treatment_1_percent_long -3L 3370451 3371600 - FBgn0027616 3371595 control_breakpoint 0.60624805294465911 0.64703056230715239 24.737291739777078 24.785958478598335 24.72955959248966 24.77557161847185 24.75965846300016 19.115611620795107 10.209598416504893 20.530594574391877 12.110393819651023 15.022501270971024 0.56409701169337378 0.70826015293577238 0.54638699420483106 0.6716801722333523 0.62238095238095237 -3L 3370451 3371600 - FBgn0027616 3371497 control_breakpoint 0.53167446986389089 0.50722931382807834 25.17339084590076 24.83086675847875 25.108450107102474 25.34486540101996 24.121432697028514 21.00523960096197 23.72215396429967 21.520352063080335 19.645096770550406 29.349412490560265 0.54513073692966096 0.51141754702049802 0.53847512564151367 0.56334489245326924 0.45111373520288744 -3L 3370451 3371600 - FBgn0027616 3371403 control_breakpoint 0.42175237278876598 0.43968252706676059 21.43265545361876 23.24127468492176 23.840243530439217 24.668855460430212 21.796132549444817 36.722792421490546 30.085068034525737 27.88682196696674 24.845774122380487 35.388813029194914 0.36854080291232694 0.43583102646276056 0.46088528899121045 0.49821347081215273 0.38115158332136839 -3L 3370451 3371600 - FBgn0027616 3371303 control_breakpoint 0.39108916961365203 0.32605616375337437 18.144907864186806 22.269351498851368 22.18854207447699 20.899986765802232 15.578958905406301 38.471119193978524 29.819508472106396 29.989017803369812 32.691946952542786 43.853564316268944 0.32049065974808444 0.42752618335797105 0.42525066573490061 0.38998381502043045 0.2621285124863183 -3L 3370451 3371600 - FBgn0027616 3371189 control_breakpoint 0.36108879385216808 0.31348344456581922 16.42870568302662 19.697783365598664 19.006203838429983 18.29248418141787 13.92595176003268 34.958610236835646 30.910044445037187 31.76652614656724 32.650427132988575 38.05812786896196 0.31970351805583574 0.38922404334965222 0.37433882015101616 0.35907810742345286 0.26788878170818553 -3L 3370451 3371600 - FBgn0027616 3370936 control_breakpoint 0.28090300350568276 0.29742764206502253 11.46529404386468 11.683852531070386 11.717151025282648 13.766111724681437 11.199166362163194 29.811874585497957 29.72761107235841 29.714773098686205 28.924812347110773 29.914478029045522 0.27776357789494338 0.28214053584193971 0.28280489678016518 0.32245991446639399 0.27239536966365108 -3L 3370451 3371600 - FBgn0027616 3371400 treatment_breakpoint 0.42145916899796149 0.43851061373185951 21.401278818382607 23.215540467097224 23.801920635167825 24.63708242685255 21.731267864203808 36.60639625382263 30.075054318450007 27.96408571339583 24.957503263330818 35.418435688866296 0.36893874460135312 0.43564048328830879 0.45979827910422255 0.49676959861626907 0.38025162884745001 -3L 3370451 3371600 - FBgn0027616 3371361 treatment_breakpoint 0.41022686556727411 0.38864357642733532 20.50124466178987 22.696466576127253 23.216860024806003 23.358299973732187 19.390276970900924 36.68975893439792 30.434754232875903 28.951959510908406 28.548944426311216 39.85531959337436 0.3584697482587354 0.42717758467694211 0.44503326376614494 0.45000077048421888 0.32728638237045177 -3L 3370451 3371600 - FBgn0027616 3371337 treatment_breakpoint 0.40286144007500929 0.35591939407775497 19.63139192604695 22.507577656074748 22.83332278545971 22.312985873192638 17.50778335689563 37.385458192346604 30.200461900984376 29.386718364840192 30.686571411834358 42.69044233657633 0.34430860149732984 0.42702361623048329 0.4372521024972148 0.42100325014405965 0.29083553801145029 -3L 3370451 3371600 - FBgn0027616 3371318 treatment_breakpoint 0.39318546325416648 0.33313189900140355 18.647118432026687 22.269249189393072 22.414766533494532 21.35928000871836 16.143664556084484 38.416093760166575 30.221344032507872 29.892123941952075 32.28006863275775 44.079936217085454 0.32678003420525586 0.42425219115453905 0.42852416440270436 0.39820170359418766 0.26806209440861944 -3L 3370451 3371600 - FBgn0027616 3371310 treatment_breakpoint 0.39141424351796555 0.32838393490616724 18.343263676520557 22.241652724683444 22.284741160633022 21.08265781222581 15.796554450012511 38.530840978593275 30.061926839480794 29.968320926900674 32.579743373440486 44.06334722928318 0.32252399906345114 0.42524150182490184 0.42647722966554374 0.3928757816721995 0.26389208814013498 -3L 3370451 3371600 - FBgn0027616 3371195 treatment_breakpoint 0.36099881812575446 0.31267620725828044 16.37902538523203 19.824462944669694 19.116066163474617 18.379188290373293 13.918532544261875 35.29630105334693 30.91506563825953 31.81586648348289 32.752884025821615 38.4250759005065 0.31696026932118287 0.39071042830578101 0.37532575675029961 0.35944540203100878 0.2659070124855521 +#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