removed additional file

scripts/new_exe_file.ipynb

-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [
-    {
-     "ename": "ModuleNotFoundError",
-     "evalue": "No module named 'rerpresentative_v4'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
-      "\u001b[1;32m/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb Cell 1\u001b[0m in \u001b[0;36m<cell line: 7>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=4'>5</a>\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mpoisson_sampling\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mps\u001b[39;00m\n\u001b[1;32m      <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=5'>6</a>\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mwritegtf\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mgt\u001b[39;00m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=6'>7</a>\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mmatch_reprtranscript_expressionlevel\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mma\u001b[39;00m\n\u001b[1;32m     <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=9'>10</a>\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mexe\u001b[39m(input_file, csv, gtf, transcript_nr):\n\u001b[1;32m     <a href='vscode-notebook-cell:/home/laura/code/transcript-sampler/scripts/new_exe_file.ipynb#W1sZmlsZQ%3D%3D?line=10'>11</a>\u001b[0m     file_name,source_pathway_name_2,deposit_pathway_name_2 \u001b[39m=\u001b[39m te\u001b[39m.\u001b[39mextract_transcript(input_file, deposit_pathway_name \u001b[39m=\u001b[39m \u001b[39mTrue\u001b[39;00m, Input_free \u001b[39m=\u001b[39m Input_free)\n",
-      "File \u001b[0;32m~/code/transcript-sampler/scripts/match_reprtranscript_expressionlevel.py:5\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mjson\u001b[39;00m\n\u001b[1;32m      4\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mre\u001b[39;00m\n\u001b[0;32m----> 5\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mrerpresentative_v4\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mrepr\u001b[39;00m\n\u001b[1;32m      6\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mos\u001b[39;00m\n\u001b[1;32m      9\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mdict_reprTrans_to_df\u001b[39m(dict_reprTrans: \u001b[39mdict\u001b[39m):\n",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'rerpresentative_v4'"
-     ]
-    }
-   ],
-   "source": [
-    "import argparse\n",
-    "import transcript_extractor as te\n",
-    "import exon_length_filter as elf\n",
-    "import representative as rtcl\n",
-    "import poisson_sampling as ps\n",
-    "import writegtf as gt\n",
-    "import match_reprtranscript_expressionlevel as ma\n",
-    "\n",
-    "\n",
-    "def exe(input_file, csv, gtf, transcript_nr):\n",
-    "    file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, deposit_pathway_name = True, Input_free = Input_free)\n",
-    "    inter_mediate_file_directory = input_file +\"_intermediate_file.txt\"\n",
-    "\n",
-    "    print(\"Transcripts are filtered based on transcript score. Please wait...\")\n",
-    "\n",
-    "    pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory)\n",
-    "\n",
-    "    print(\"Transcripts filtered\\n\")\n",
-    "    elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = True)\n",
-    "\n",
-    "    tsv_input = ma.output_tsv()\n",
-    "    print(\"Poisson sampling of transcripts\")\n",
-    "    ps.transcript_sampling(transcript_nr, tsv_input, csv)\n",
-    "    print(\"output csv file ready\")\n",
-    "    \n",
-    "    print(\"writing output gtf file\")\n",
-    "    gt.gtf_file_writer(input_file, csv, gtf)\n",
-    "\n",
-    "\n",
-    "\n",
-    "if __name__ == '__main__':\n",
-    "    parser = argparse.ArgumentParser(\n",
-    "        description=\"transcript sampler\",\n",
-    "        formatter_class=argparse.ArgumentDefaultsHelpFormatter\n",
-    "    )\n",
-    "    parser.add_argument(\"--annotation\", required=True, help=\"gtf file with genome annotation\")\n",
-    "    parser.add_argument(\"--output_csv\", required=True, help=\"output csv file\")\n",
-    "    parser.add_argument(\"--output_gtf\", required=True, help=\"output gtf file\")\n",
-    "    parser.add_argument(\"--transcript_number\", required=True, help=\"total number of transcripts to sample\")\n",
-    "    args = parser.parse_args()\n",
-    "    exe(args.annotation, args.output_csv, args.output_gtf, args.transcript_nr)\n",
-    "\n",
-    "    #return(file_name,source_pathway_name,deposit_pathway_name)\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3.9.12 ('nextstrain')",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.12"
-  },
-  "orig_nbformat": 4,
-  "vscode": {
-   "interpreter": {
-    "hash": "41a54f34eee8c9e478b3404dd74579d3248e5c82a4969468d7042e338229b1fe"
-   }
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}