diff --git a/PPRCODE.ipynb b/PPRCODE.ipynb index 38629c3..3514171 100644 --- a/PPRCODE.ipynb +++ b/PPRCODE.ipynb @@ -6,7 +6,7 @@ "name": "PPRCODE_dev.ipynb", "provenance": [], "collapsed_sections": [], - "authorship_tag": "ABX9TyP2yBx9QHv5Fqu29zdtOBtp", + "authorship_tag": "ABX9TyNL/nVnTG63Ck1Blznoj5AZ", "include_colab_link": true }, "kernelspec": { @@ -18,7 +18,7 @@ }, "widgets": { "application/vnd.jupyter.widget-state+json": { - "6261af9abf6c41858464d503b3c45537": { + "565afb32daa742f8a53e66eb72483a62": { "model_module": "@jupyter-widgets/controls", "model_name": "HBoxModel", "model_module_version": "1.5.0", @@ -31,16 +31,16 @@ "_view_count": null, "_view_module_version": "1.5.0", "box_style": "", - "layout": "IPY_MODEL_4a1dc386626549bab0a4127a545b00d2", + "layout": "IPY_MODEL_4713b6c3a3f3497b94f5d288f1a77622", "_model_module": "@jupyter-widgets/controls", "children": [ - "IPY_MODEL_555e25281f4a427db4bf1e29b501b705", - "IPY_MODEL_dbeb6a2d72f346898123e23268287734", - "IPY_MODEL_f2e8c979f3fb49c4a7fb3152af444f9c" + "IPY_MODEL_f6b3a738ff01416a89e1945fa7b93774", + "IPY_MODEL_da6d43ba61324b508281f495d9586434", + "IPY_MODEL_92d3e09255ed4e3cae4d434a919ff360" ] } }, - 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"layout": "IPY_MODEL_d181366c12b84a49a172931292f4543d" + "layout": "IPY_MODEL_c36f440c4917448eb372f38a1c3bde09" } }, - "eb42a9b04f0243ee929691b096d137c4": { + "2448833d883043a38e880034bd95bd79": { "model_module": "@jupyter-widgets/controls", "model_name": "DescriptionStyleModel", "model_module_version": "1.5.0", @@ -173,7 +173,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "28d211688a9d49f6a9ea0cf8a4db4760": { + "2d119896c2a345e4942e1d7ecaf857ae": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -225,7 +225,7 @@ "left": null } }, - "169b4d423dc743e6bba8307c4947754c": { + "2fb362b32f2b404490be8293d15e0afa": { "model_module": "@jupyter-widgets/controls", "model_name": "ProgressStyleModel", "model_module_version": "1.5.0", @@ -241,7 +241,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "259f0109f07d4ea6a37c195d971c9f31": { + "29e3e12cd2c54228afe60b2b35f0c0ab": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -293,7 +293,7 @@ "left": null } }, - 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"layout": "IPY_MODEL_b402c2187fb3402798f7f6ae47362a5a" + "layout": "IPY_MODEL_4e0ed785a16b4372b7520321a1d400cd" } }, - "41e1a2b062564d39a09477241de6250e": { + "97a8e8890c984b5d97bdad66a8ea2cc3": { "model_module": "@jupyter-widgets/controls", "model_name": "DescriptionStyleModel", "model_module_version": "1.5.0", @@ -857,7 +857,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "def348a1ba884174b3f48e6d812e9471": { + "18cf1b3683f54959adeb04824a350109": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -909,7 +909,7 @@ "left": null } }, - "9e52f4a04447433ab871b4ae0e55f30d": { + "3ff323598b8a41db8903b29e8c3bad62": { "model_module": "@jupyter-widgets/controls", "model_name": "ProgressStyleModel", "model_module_version": "1.5.0", @@ -925,7 +925,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "631596daa3184ab6a511e9cdce3e9228": { + "77c9ec995fb0464ba397e16ae61cdb2e": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -977,7 +977,7 @@ "left": null } }, - 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"918d926688b84e3ea938302e68c91a7b": { + "b88ae2beee5442959a5aba057918cf90": { "model_module": "@jupyter-widgets/controls", "model_name": "FloatProgressModel", "model_module_version": "1.5.0", "state": { "_view_name": "ProgressView", - "style": "IPY_MODEL_a6b14a719c7647958b3b37d2bec2d6df", + "style": "IPY_MODEL_27e94ca1d71c483fbf34e054a198a4a7", "_dom_classes": [], "description": "", "_model_name": "FloatProgressModel", @@ -1160,16 +1160,16 @@ "min": 0, "description_tooltip": null, "_model_module": "@jupyter-widgets/controls", - "layout": "IPY_MODEL_214d2e42847546b58479e5db0e4e725d" + "layout": "IPY_MODEL_7bfa2765a8a448b78d662e7033ef88c3" } }, - "2c458842a6ef481c95d9ebd028ee32b9": { + "63c4aaf4a7654815b173e06f70b2f55e": { "model_module": "@jupyter-widgets/controls", "model_name": "HTMLModel", "model_module_version": "1.5.0", "state": { "_view_name": "HTMLView", - "style": "IPY_MODEL_a8bdeab8b572400f881fd5323c344593", + "style": "IPY_MODEL_b462cb176cd7453fa8cee93a10bc9d8e", "_dom_classes": [], "description": "", "_model_name": "HTMLModel", @@ -1181,10 +1181,10 @@ "_view_module_version": "1.5.0", "description_tooltip": null, "_model_module": "@jupyter-widgets/controls", - "layout": "IPY_MODEL_d296555415f848c199fc9f16d7b252af" + "layout": "IPY_MODEL_e345f5cd1d2948388bcaf6e99e9f6353" } }, - "35cf9cebd10c41ddb9e4cd2e64433f6d": { + "52aa466ba0344c9ea43289fd7a1a0b84": { "model_module": "@jupyter-widgets/controls", "model_name": "DescriptionStyleModel", "model_module_version": "1.5.0", @@ -1199,7 +1199,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "1e24be247568458fb5e8e1a240097989": { + "f180820b494d429c81c381ec2a1a9aae": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -1251,7 +1251,7 @@ "left": null } }, - "a6b14a719c7647958b3b37d2bec2d6df": { + "27e94ca1d71c483fbf34e054a198a4a7": { "model_module": "@jupyter-widgets/controls", "model_name": "ProgressStyleModel", "model_module_version": "1.5.0", @@ -1267,7 +1267,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "214d2e42847546b58479e5db0e4e725d": { + "7bfa2765a8a448b78d662e7033ef88c3": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -1319,7 +1319,7 @@ "left": null } }, - "a8bdeab8b572400f881fd5323c344593": { + "b462cb176cd7453fa8cee93a10bc9d8e": { "model_module": "@jupyter-widgets/controls", "model_name": "DescriptionStyleModel", "model_module_version": "1.5.0", @@ -1334,7 +1334,7 @@ "_model_module": "@jupyter-widgets/controls" } }, - "d296555415f848c199fc9f16d7b252af": { + "e345f5cd1d2948388bcaf6e99e9f6353": { "model_module": "@jupyter-widgets/base", "model_name": "LayoutModel", "model_module_version": "1.2.0", @@ -1428,21 +1428,21 @@ "base_uri": "https://localhost:8080/", "height": 49, "referenced_widgets": [ - "6261af9abf6c41858464d503b3c45537", - "4a1dc386626549bab0a4127a545b00d2", - "555e25281f4a427db4bf1e29b501b705", - "dbeb6a2d72f346898123e23268287734", - "f2e8c979f3fb49c4a7fb3152af444f9c", - "eb42a9b04f0243ee929691b096d137c4", - "28d211688a9d49f6a9ea0cf8a4db4760", - "169b4d423dc743e6bba8307c4947754c", - "259f0109f07d4ea6a37c195d971c9f31", - "a1d996cf1fde4306b66d09cadc1d1776", - "d181366c12b84a49a172931292f4543d" + "565afb32daa742f8a53e66eb72483a62", + "4713b6c3a3f3497b94f5d288f1a77622", + "f6b3a738ff01416a89e1945fa7b93774", + "da6d43ba61324b508281f495d9586434", + "92d3e09255ed4e3cae4d434a919ff360", + "2448833d883043a38e880034bd95bd79", + "2d119896c2a345e4942e1d7ecaf857ae", + "2fb362b32f2b404490be8293d15e0afa", + "29e3e12cd2c54228afe60b2b35f0c0ab", + "b5286cbab3874e5f8bc1448873ffd3a9", + "c36f440c4917448eb372f38a1c3bde09" ] }, "cellView": "form", - "outputId": "120d995a-615a-48db-fbd2-7bb1d970b54e" + "outputId": "c600c110-393f-43e5-ac61-63c6e1d3a2fb" }, "source": [ "#@title Install packages\n", @@ -1753,7 +1753,7 @@ "output_type": "display_data", "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "6261af9abf6c41858464d503b3c45537", + "model_id": "565afb32daa742f8a53e66eb72483a62", "version_minor": 0, "version_major": 2 }, @@ -1859,22 +1859,22 @@ "base_uri": "https://localhost:8080/", "height": 49, "referenced_widgets": [ - "2c3d8dc08c674521a9d64a757e17fea9", - "0a49f39abd0a46c19c2fa200651b6581", - "a86e4d813bc54a989120d5bda442dc58", - "d807a190231d4d258f77836a2a44358c", - "d444517f089e46e2b21455511a812a74", - "8602d76755894e07b28aee032898bb27", - "85cb29bc9b7d4a579b9b7b28288a1ff9", - "1e620ce10c6546398d957d62d9b89179", - "56626bb5aa6343eda8f8dd096e7eb8f6", - "6008a184ae3c4aafaa4506482350d95c", - "a91ff8b5f9ca4486a1fa18afb4100bb8" + "905a02b4dfa54b2696ecf69f70f219f5", + "bf1355a12ebf40ceb70e955485fe1910", + "526c04c6585f4539a8e9455c81220b1f", + "3416db311fc14657aed83d46c0ff294e", + "872eacb6675b4777a2f97ac00f0cc6bd", + "b4baee759ae8438e948b17df869c1611", + "dacf2d488a16447eb002c317f864c493", + "43d4d72b6c9b417aa9beaf88d07031bf", + "053cdc1cbecc4910ad5ea0a39503fa84", + "a37d43ddd2b545f5b259b2ff67f42f7d", + "4a39d2debf4845478cc305da5f9b0a70" ] }, "id": "LQ5Kdj0pCzAV", "cellView": "form", - "outputId": "cd888e2f-a92c-427e-abed-1167e32773a1" + "outputId": "3518ea9a-5a27-43a7-db53-a14eafd5eda4" }, "source": [ "#@title Process the FASTAs\n", @@ -1905,7 +1905,7 @@ "output_type": "display_data", "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2c3d8dc08c674521a9d64a757e17fea9", + "model_id": "905a02b4dfa54b2696ecf69f70f219f5", "version_minor": 0, "version_major": 2 }, @@ -1922,24 +1922,24 @@ "metadata": { "colab": { "base_uri": "https://localhost:8080/", - "height": 551, + "height": 604, "referenced_widgets": [ - "59046fbb57af40f3852c2b2f48b95b24", - "87e63e0e2e2c489fa6b03f69fb0b6237", - "7009b02da4e64bd5b4795df8fa3a5ae9", - "41b5ffea974a49069c689fcef73c94c7", - "9531478792264c088a04aefc7e987e6a", - "41e1a2b062564d39a09477241de6250e", - "def348a1ba884174b3f48e6d812e9471", - "9e52f4a04447433ab871b4ae0e55f30d", - "631596daa3184ab6a511e9cdce3e9228", - "e781220fb38543d0b8bd8b6f30b97328", - "b402c2187fb3402798f7f6ae47362a5a" + "509a8b64cca64f5bb3cfe4da0fe6b2da", + "a0c534f345354334846de74706c96107", + "f2167e736199447da2994aca964d6737", + "7045fea74fa2487ebe472c55e2088954", + "74fb6e171129486bbce9664fd98718d9", + "97a8e8890c984b5d97bdad66a8ea2cc3", + "18cf1b3683f54959adeb04824a350109", + "3ff323598b8a41db8903b29e8c3bad62", + "77c9ec995fb0464ba397e16ae61cdb2e", + "3a9c2614ee8b4bb08b3a8ff94b8ed234", + "4e0ed785a16b4372b7520321a1d400cd" ] }, "id": "G-1aryIPoR3u", "cellView": "form", - "outputId": "31a4c4e2-4b37-4157-9486-d44e23140bfb" + "outputId": "af5d3af1-997e-4409-ba13-8f76e5bcb043" }, "source": [ "#@title Plot PPRs\n", @@ -2000,16 +2000,17 @@ " print(f'score maxima: {max(scores)}')\n", " if color_scale==0:color_scale=max(scores)\n", "\n", + " what_to_plot=[]\n", + " if plot_ppr: what_to_plot.append('Motif')\n", + " if plot_rna: what_to_plot.append('RNA')\n", + " if plot_score: what_to_plot.append('Score')\n", + " if plot_edge: what_to_plot.append('Edge')\n", + " if plot_type and program=='PPRfinder': what_to_plot.append('Type')\n", + "\n", " for s in job_list.keys():\n", " data = pickle.load(open(f'{RES_DIR_PICKLE}/{s}.pkl','rb'))\n", " #print(s)\n", " try:\n", - " what_to_plot=[]\n", - " if plot_ppr: what_to_plot.append('Motif')\n", - " if plot_rna: what_to_plot.append('RNA')\n", - " if plot_score: what_to_plot.append('Score')\n", - " if plot_edge: what_to_plot.append('Edge')\n", - " if plot_type and program=='PPRfinder': what_to_plot.append('Type')\n", " draw_my_ppr(job_list[s],data,what_to_plot)\n", " except Exception as e:\n", " traceback.print_exc() #if debug else print(e)\n", @@ -2022,7 +2023,7 @@ "output_type": "display_data", "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "59046fbb57af40f3852c2b2f48b95b24", + "model_id": "509a8b64cca64f5bb3cfe4da0fe6b2da", "version_minor": 0, "version_major": 2 }, @@ -2080,21 +2081,21 @@ "base_uri": "https://localhost:8080/", "height": 66, "referenced_widgets": [ - "d1ce36a9a691459eba7a56d7c8c5ddae", - "3d00ec9619384d9a932eaf0ca5b801cb", - "f85a1c47826d4362a97a36313599c8be", - "918d926688b84e3ea938302e68c91a7b", - "2c458842a6ef481c95d9ebd028ee32b9", - "35cf9cebd10c41ddb9e4cd2e64433f6d", - "1e24be247568458fb5e8e1a240097989", - "a6b14a719c7647958b3b37d2bec2d6df", - "214d2e42847546b58479e5db0e4e725d", - "a8bdeab8b572400f881fd5323c344593", - "d296555415f848c199fc9f16d7b252af" + "d440571a8b7c46669c5ef874362728af", + "e4739439be7e4d81a8618c65c4cfb7d1", + "35cad027fdea4ab083b485c32d1e66b2", + "b88ae2beee5442959a5aba057918cf90", + "63c4aaf4a7654815b173e06f70b2f55e", + "52aa466ba0344c9ea43289fd7a1a0b84", + "f180820b494d429c81c381ec2a1a9aae", + "27e94ca1d71c483fbf34e054a198a4a7", + "7bfa2765a8a448b78d662e7033ef88c3", + "b462cb176cd7453fa8cee93a10bc9d8e", + "e345f5cd1d2948388bcaf6e99e9f6353" ] }, "cellView": "form", - "outputId": "f35b85be-97fd-4946-cd9e-c24c2d863dec" + "outputId": "950c4235-61bd-4995-871d-a8d580431929" }, "source": [ "#@title Generate report and download it!\n", @@ -2264,7 +2265,7 @@ "output_type": "display_data", "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d1ce36a9a691459eba7a56d7c8c5ddae", + "model_id": "d440571a8b7c46669c5ef874362728af", "version_minor": 0, "version_major": 2 }, @@ -2337,7 +2338,7 @@ "output_type": "display_data", "data": { "application/javascript": [ - "download(\"download_e1d99a57-dc8f-46fc-b830-18d449f3c3ab\", \"PPRCODE_20211123_050452.zip\", 80253)" + "download(\"download_d7c368b0-ed5d-4939-8c96-31ed6c5395b2\", \"PPRCODE_20211123_060132.zip\", 80252)" ], "text/plain": [ ""