{ "cells": [ { "cell_type": "markdown", "id": "f8274b0b-7857-4940-9e11-5e640284f48a", "metadata": {}, "source": [ "point of this notebook is to make a txt file that will provide the entire track description and data so that the user doesn't need to do it each time \n", "so far it's just an interactive notebook - maybe it'll be added to the BEDtoBW_script.sh one day but for now this'll do the job\n", "\n", "track info to add:\n", "* track type=bigWig\n", "* name=\"GABAergic_Dp16_yng\"\n", "* description=\"A Graph of Data from My Lab\"\n", "* autoScale=off\n", "* bigDataUrl=https://epigenomics.sdsc.edu/kdang/ASAP_proj/Aging_DASeq_broadCT/splitfrags_out_GABAergic_byCond/GABAergic_Dp16_yng_sort.bw\n", "\n", "NOTE - name and description is the same; bigDataUrl will need to be edited based on where the bigwigs are in the VM\n", "\n", "URL to bw - https://epigenomics.sdsc.edu/kdang/ASAP_proj/GenBrow_broadCT_byCond/ucscBigWig_out/" ] }, { "cell_type": "code", "execution_count": 9, "id": "ab97497b-94cd-4801-a355-fe9da460d382", "metadata": {}, "outputs": [], "source": [ "library(stringr)" ] }, { "cell_type": "code", "execution_count": 15, "id": "4a52fef6-5e89-40e4-9b1f-90b5ffaf654a", "metadata": {}, "outputs": [], "source": [ "bw.path <- \"/tscc/projects/ps-epigen/users/kdang/ASAP/GenBrow_broadCT_byCond/ucscBigWig_out/\"\n", "opath <- \"/tscc/projects/ps-epigen/users/kdang/ASAP/GenBrow_broadCT_byCond/\"" ] }, { "cell_type": "code", "execution_count": 8, "id": "9143075a-96e7-4938-9a83-f1f8b8d59af4", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. '2N_old_Astrocyte_sort.bw'
  2. '2N_old_BFCN_sort.bw'
  3. '2N_old_GABAergic_sort.bw'
  4. '2N_old_Glutamatergic_sort.bw'
  5. '2N_old_Microglia_sort.bw'
  6. '2N_old_Oligodendrocyte_sort.bw'
  7. '2N_old_OPC_sort.bw'
  8. '2N_yng_Astrocyte_sort.bw'
  9. '2N_yng_BFCN_sort.bw'
  10. '2N_yng_GABAergic_sort.bw'
  11. '2N_yng_Glutamatergic_sort.bw'
  12. '2N_yng_Microglia_sort.bw'
  13. '2N_yng_Oligodendrocyte_sort.bw'
  14. '2N_yng_OPC_sort.bw'
  15. 'Dp16_old_Astrocyte_sort.bw'
  16. 'Dp16_old_BFCN_sort.bw'
  17. 'Dp16_old_GABAergic_sort.bw'
  18. 'Dp16_old_Glutamatergic_sort.bw'
  19. 'Dp16_old_Microglia_sort.bw'
  20. 'Dp16_old_Oligodendrocyte_sort.bw'
  21. 'Dp16_old_OPC_sort.bw'
  22. 'Dp16_yng_Astrocyte_sort.bw'
  23. 'Dp16_yng_BFCN_sort.bw'
  24. 'Dp16_yng_GABAergic_sort.bw'
  25. 'Dp16_yng_Glutamatergic_sort.bw'
  26. 'Dp16_yng_Microglia_sort.bw'
  27. 'Dp16_yng_Oligodendrocyte_sort.bw'
  28. 'Dp16_yng_OPC_sort.bw'
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item '2N\\_old\\_Astrocyte\\_sort.bw'\n", "\\item '2N\\_old\\_BFCN\\_sort.bw'\n", "\\item '2N\\_old\\_GABAergic\\_sort.bw'\n", "\\item '2N\\_old\\_Glutamatergic\\_sort.bw'\n", "\\item '2N\\_old\\_Microglia\\_sort.bw'\n", "\\item '2N\\_old\\_Oligodendrocyte\\_sort.bw'\n", "\\item '2N\\_old\\_OPC\\_sort.bw'\n", "\\item '2N\\_yng\\_Astrocyte\\_sort.bw'\n", "\\item '2N\\_yng\\_BFCN\\_sort.bw'\n", "\\item '2N\\_yng\\_GABAergic\\_sort.bw'\n", "\\item '2N\\_yng\\_Glutamatergic\\_sort.bw'\n", "\\item '2N\\_yng\\_Microglia\\_sort.bw'\n", "\\item '2N\\_yng\\_Oligodendrocyte\\_sort.bw'\n", "\\item '2N\\_yng\\_OPC\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Astrocyte\\_sort.bw'\n", "\\item 'Dp16\\_old\\_BFCN\\_sort.bw'\n", "\\item 'Dp16\\_old\\_GABAergic\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Glutamatergic\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Microglia\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Oligodendrocyte\\_sort.bw'\n", "\\item 'Dp16\\_old\\_OPC\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Astrocyte\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_BFCN\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_GABAergic\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Glutamatergic\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Microglia\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Oligodendrocyte\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_OPC\\_sort.bw'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. '2N_old_Astrocyte_sort.bw'\n", "2. '2N_old_BFCN_sort.bw'\n", "3. '2N_old_GABAergic_sort.bw'\n", "4. '2N_old_Glutamatergic_sort.bw'\n", "5. '2N_old_Microglia_sort.bw'\n", "6. '2N_old_Oligodendrocyte_sort.bw'\n", "7. '2N_old_OPC_sort.bw'\n", "8. '2N_yng_Astrocyte_sort.bw'\n", "9. '2N_yng_BFCN_sort.bw'\n", "10. '2N_yng_GABAergic_sort.bw'\n", "11. '2N_yng_Glutamatergic_sort.bw'\n", "12. '2N_yng_Microglia_sort.bw'\n", "13. '2N_yng_Oligodendrocyte_sort.bw'\n", "14. '2N_yng_OPC_sort.bw'\n", "15. 'Dp16_old_Astrocyte_sort.bw'\n", "16. 'Dp16_old_BFCN_sort.bw'\n", "17. 'Dp16_old_GABAergic_sort.bw'\n", "18. 'Dp16_old_Glutamatergic_sort.bw'\n", "19. 'Dp16_old_Microglia_sort.bw'\n", "20. 'Dp16_old_Oligodendrocyte_sort.bw'\n", "21. 'Dp16_old_OPC_sort.bw'\n", "22. 'Dp16_yng_Astrocyte_sort.bw'\n", "23. 'Dp16_yng_BFCN_sort.bw'\n", "24. 'Dp16_yng_GABAergic_sort.bw'\n", "25. 'Dp16_yng_Glutamatergic_sort.bw'\n", "26. 'Dp16_yng_Microglia_sort.bw'\n", "27. 'Dp16_yng_Oligodendrocyte_sort.bw'\n", "28. 'Dp16_yng_OPC_sort.bw'\n", "\n", "\n" ], "text/plain": [ " [1] \"2N_old_Astrocyte_sort.bw\" \"2N_old_BFCN_sort.bw\" \n", " [3] \"2N_old_GABAergic_sort.bw\" \"2N_old_Glutamatergic_sort.bw\" \n", " [5] \"2N_old_Microglia_sort.bw\" \"2N_old_Oligodendrocyte_sort.bw\" \n", " [7] \"2N_old_OPC_sort.bw\" \"2N_yng_Astrocyte_sort.bw\" \n", " [9] \"2N_yng_BFCN_sort.bw\" \"2N_yng_GABAergic_sort.bw\" \n", "[11] \"2N_yng_Glutamatergic_sort.bw\" \"2N_yng_Microglia_sort.bw\" \n", "[13] \"2N_yng_Oligodendrocyte_sort.bw\" \"2N_yng_OPC_sort.bw\" \n", "[15] \"Dp16_old_Astrocyte_sort.bw\" \"Dp16_old_BFCN_sort.bw\" \n", "[17] \"Dp16_old_GABAergic_sort.bw\" \"Dp16_old_Glutamatergic_sort.bw\" \n", "[19] \"Dp16_old_Microglia_sort.bw\" \"Dp16_old_Oligodendrocyte_sort.bw\"\n", "[21] \"Dp16_old_OPC_sort.bw\" \"Dp16_yng_Astrocyte_sort.bw\" \n", "[23] \"Dp16_yng_BFCN_sort.bw\" \"Dp16_yng_GABAergic_sort.bw\" \n", "[25] \"Dp16_yng_Glutamatergic_sort.bw\" \"Dp16_yng_Microglia_sort.bw\" \n", "[27] \"Dp16_yng_Oligodendrocyte_sort.bw\" \"Dp16_yng_OPC_sort.bw\" " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "
  1. '2N_old_Astrocyte_sort.bw'
  2. '2N_yng_Astrocyte_sort.bw'
  3. 'Dp16_old_Astrocyte_sort.bw'
  4. 'Dp16_yng_Astrocyte_sort.bw'
  5. '2N_old_BFCN_sort.bw'
  6. '2N_yng_BFCN_sort.bw'
  7. 'Dp16_old_BFCN_sort.bw'
  8. 'Dp16_yng_BFCN_sort.bw'
  9. '2N_old_GABAergic_sort.bw'
  10. '2N_yng_GABAergic_sort.bw'
  11. 'Dp16_old_GABAergic_sort.bw'
  12. 'Dp16_yng_GABAergic_sort.bw'
  13. '2N_old_Glutamatergic_sort.bw'
  14. '2N_yng_Glutamatergic_sort.bw'
  15. 'Dp16_old_Glutamatergic_sort.bw'
  16. 'Dp16_yng_Glutamatergic_sort.bw'
  17. '2N_old_Microglia_sort.bw'
  18. '2N_yng_Microglia_sort.bw'
  19. 'Dp16_old_Microglia_sort.bw'
  20. 'Dp16_yng_Microglia_sort.bw'
  21. '2N_old_Oligodendrocyte_sort.bw'
  22. '2N_yng_Oligodendrocyte_sort.bw'
  23. 'Dp16_old_Oligodendrocyte_sort.bw'
  24. 'Dp16_yng_Oligodendrocyte_sort.bw'
  25. '2N_old_OPC_sort.bw'
  26. '2N_yng_OPC_sort.bw'
  27. 'Dp16_old_OPC_sort.bw'
  28. 'Dp16_yng_OPC_sort.bw'
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item '2N\\_old\\_Astrocyte\\_sort.bw'\n", "\\item '2N\\_yng\\_Astrocyte\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Astrocyte\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Astrocyte\\_sort.bw'\n", "\\item '2N\\_old\\_BFCN\\_sort.bw'\n", "\\item '2N\\_yng\\_BFCN\\_sort.bw'\n", "\\item 'Dp16\\_old\\_BFCN\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_BFCN\\_sort.bw'\n", "\\item '2N\\_old\\_GABAergic\\_sort.bw'\n", "\\item '2N\\_yng\\_GABAergic\\_sort.bw'\n", "\\item 'Dp16\\_old\\_GABAergic\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_GABAergic\\_sort.bw'\n", "\\item '2N\\_old\\_Glutamatergic\\_sort.bw'\n", "\\item '2N\\_yng\\_Glutamatergic\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Glutamatergic\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Glutamatergic\\_sort.bw'\n", "\\item '2N\\_old\\_Microglia\\_sort.bw'\n", "\\item '2N\\_yng\\_Microglia\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Microglia\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Microglia\\_sort.bw'\n", "\\item '2N\\_old\\_Oligodendrocyte\\_sort.bw'\n", "\\item '2N\\_yng\\_Oligodendrocyte\\_sort.bw'\n", "\\item 'Dp16\\_old\\_Oligodendrocyte\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_Oligodendrocyte\\_sort.bw'\n", "\\item '2N\\_old\\_OPC\\_sort.bw'\n", "\\item '2N\\_yng\\_OPC\\_sort.bw'\n", "\\item 'Dp16\\_old\\_OPC\\_sort.bw'\n", "\\item 'Dp16\\_yng\\_OPC\\_sort.bw'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. '2N_old_Astrocyte_sort.bw'\n", "2. '2N_yng_Astrocyte_sort.bw'\n", "3. 'Dp16_old_Astrocyte_sort.bw'\n", "4. 'Dp16_yng_Astrocyte_sort.bw'\n", "5. '2N_old_BFCN_sort.bw'\n", "6. '2N_yng_BFCN_sort.bw'\n", "7. 'Dp16_old_BFCN_sort.bw'\n", "8. 'Dp16_yng_BFCN_sort.bw'\n", "9. '2N_old_GABAergic_sort.bw'\n", "10. '2N_yng_GABAergic_sort.bw'\n", "11. 'Dp16_old_GABAergic_sort.bw'\n", "12. 'Dp16_yng_GABAergic_sort.bw'\n", "13. '2N_old_Glutamatergic_sort.bw'\n", "14. '2N_yng_Glutamatergic_sort.bw'\n", "15. 'Dp16_old_Glutamatergic_sort.bw'\n", "16. 'Dp16_yng_Glutamatergic_sort.bw'\n", "17. '2N_old_Microglia_sort.bw'\n", "18. '2N_yng_Microglia_sort.bw'\n", "19. 'Dp16_old_Microglia_sort.bw'\n", "20. 'Dp16_yng_Microglia_sort.bw'\n", "21. '2N_old_Oligodendrocyte_sort.bw'\n", "22. '2N_yng_Oligodendrocyte_sort.bw'\n", "23. 'Dp16_old_Oligodendrocyte_sort.bw'\n", "24. 'Dp16_yng_Oligodendrocyte_sort.bw'\n", "25. '2N_old_OPC_sort.bw'\n", "26. '2N_yng_OPC_sort.bw'\n", "27. 'Dp16_old_OPC_sort.bw'\n", "28. 'Dp16_yng_OPC_sort.bw'\n", "\n", "\n" ], "text/plain": [ " [1] \"2N_old_Astrocyte_sort.bw\" \"2N_yng_Astrocyte_sort.bw\" \n", " [3] \"Dp16_old_Astrocyte_sort.bw\" \"Dp16_yng_Astrocyte_sort.bw\" \n", " [5] \"2N_old_BFCN_sort.bw\" \"2N_yng_BFCN_sort.bw\" \n", " [7] \"Dp16_old_BFCN_sort.bw\" \"Dp16_yng_BFCN_sort.bw\" \n", " [9] \"2N_old_GABAergic_sort.bw\" \"2N_yng_GABAergic_sort.bw\" \n", "[11] \"Dp16_old_GABAergic_sort.bw\" \"Dp16_yng_GABAergic_sort.bw\" \n", "[13] \"2N_old_Glutamatergic_sort.bw\" \"2N_yng_Glutamatergic_sort.bw\" \n", "[15] \"Dp16_old_Glutamatergic_sort.bw\" \"Dp16_yng_Glutamatergic_sort.bw\" \n", "[17] \"2N_old_Microglia_sort.bw\" \"2N_yng_Microglia_sort.bw\" \n", "[19] \"Dp16_old_Microglia_sort.bw\" \"Dp16_yng_Microglia_sort.bw\" \n", "[21] \"2N_old_Oligodendrocyte_sort.bw\" \"2N_yng_Oligodendrocyte_sort.bw\" \n", "[23] \"Dp16_old_Oligodendrocyte_sort.bw\" \"Dp16_yng_Oligodendrocyte_sort.bw\"\n", "[25] \"2N_old_OPC_sort.bw\" \"2N_yng_OPC_sort.bw\" \n", "[27] \"Dp16_old_OPC_sort.bw\" \"Dp16_yng_OPC_sort.bw\" " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "bw.files <- list.files(bw.path, pattern = \".bw\")\n", "bw.files\n", "\n", "# NOTE - ALL OF THIS SORTING ISN'T NEEDED I JUST DO IT BC IT MAKES IT EASIER FOR USER\n", "# sort by celltype since right now its just sorted by conditions\n", "celltypes <- c(\"Astrocyte\", \"BFCN\", \"GABAergic\", \"Glutamatergic\", \"Microglia\", \"Oligodendrocyte\", \"OPC\")\n", "sort.bw.files <- bw.files[order(sapply(bw.files, function(x) min(which(sapply(celltypes, grepl, x)))))]\n", "sort.bw.files" ] }, { "cell_type": "code", "execution_count": 18, "id": "ec9b3d21-1d48-4038-925d-dc667a5bda3a", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[1] \"2N_old_Astrocyte_sort.bw\"\n", "[1] \"2N_yng_Astrocyte_sort.bw\"\n", "[1] \"Dp16_old_Astrocyte_sort.bw\"\n", "[1] \"Dp16_yng_Astrocyte_sort.bw\"\n", "[1] \"2N_old_BFCN_sort.bw\"\n", "[1] \"2N_yng_BFCN_sort.bw\"\n", "[1] \"Dp16_old_BFCN_sort.bw\"\n", "[1] \"Dp16_yng_BFCN_sort.bw\"\n", "[1] \"2N_old_GABAergic_sort.bw\"\n", "[1] \"2N_yng_GABAergic_sort.bw\"\n", "[1] \"Dp16_old_GABAergic_sort.bw\"\n", "[1] \"Dp16_yng_GABAergic_sort.bw\"\n", "[1] \"2N_old_Glutamatergic_sort.bw\"\n", "[1] \"2N_yng_Glutamatergic_sort.bw\"\n", "[1] \"Dp16_old_Glutamatergic_sort.bw\"\n", "[1] \"Dp16_yng_Glutamatergic_sort.bw\"\n", "[1] \"2N_old_Microglia_sort.bw\"\n", "[1] \"2N_yng_Microglia_sort.bw\"\n", "[1] \"Dp16_old_Microglia_sort.bw\"\n", "[1] \"Dp16_yng_Microglia_sort.bw\"\n", "[1] \"2N_old_Oligodendrocyte_sort.bw\"\n", "[1] \"2N_yng_Oligodendrocyte_sort.bw\"\n", "[1] \"Dp16_old_Oligodendrocyte_sort.bw\"\n", "[1] \"Dp16_yng_Oligodendrocyte_sort.bw\"\n", "[1] \"2N_old_OPC_sort.bw\"\n", "[1] \"2N_yng_OPC_sort.bw\"\n", "[1] \"Dp16_old_OPC_sort.bw\"\n", "[1] \"Dp16_yng_OPC_sort.bw\"\n" ] } ], "source": [ "trackTxt <- c()\n", "\n", "for(bw in sort.bw.files){\n", " print(bw)\n", "\n", " basename <- str_remove(bw, pattern = \".bw\")\n", "\n", " addTrack <- paste0(\"track type=bigWig name=\\\"\",str_remove(basename, \"_sort\"),\"\\\" description=\\\"\",str_remove(basename, \"_sort\"),\"\\\" autoScale=off bigDataUrl=\",\n", " \"https://epigenomics.sdsc.edu/kdang/ASAP_proj/GenBrow_broadCT_byCond/ucscBigWig_out/\",basename,\".bw\")\n", " trackTxt <- c(trackTxt, addTrack)\n", "}\n", "\n", "#write.table(trackTxt, paste0(opath, \"ucscTrackInfo.txt\"), quote = FALSE, row.names = FALSE, col.names = FALSE)" ] } ], "metadata": { "kernelspec": { "display_name": "R", "language": "R", "name": "ir" }, "language_info": { "codemirror_mode": "r", "file_extension": ".r", "mimetype": "text/x-r-source", "name": "R", "pygments_lexer": "r", "version": "4.3.1" } }, "nbformat": 4, "nbformat_minor": 5 }