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Commit ce3dce3

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Update Unix Jupyter notebook Markdown lecture
- Add start up instructions - Change double quotes for single quotes when necessary. - Add exercise breaks - Add hints to exercises
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‎notebooks/unix_outline_md.ipynb‎

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@@ -11,6 +11,27 @@
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"# Linux/Unix Command and Bash Scripting (Markdown Code Blocks)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Getting Started\n",
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"\n",
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"This lecture can be found on `state`.\n",
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"\n",
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"Let's all SSH into `state`.\n",
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"\n",
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"```sh\n",
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"ssh leunge@state.ohsu.edu\n",
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"```\n",
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"\n",
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"And navigate to your folder.\n",
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"\n",
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"```sh\n",
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"cd /home/courses/BMI565/students\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
@@ -67,47 +88,37 @@
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"heading_collapsed": true
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},
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"metadata": {},
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"source": [
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"#### `pwd`"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"hidden": true
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},
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"metadata": {},
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"source": [
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"You can use `pwd` to show you where you are in your computer."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"hidden": true
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"pwd"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"heading_collapsed": true
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},
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"metadata": {},
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"source": [
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"#### `ls`"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"hidden": true
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},
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"metadata": {},
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"source": [
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"After knowing where you are, you should find out what files and directories are around you.\n",
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"\n",
@@ -126,7 +137,6 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"hidden": true,
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"scrolled": false
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},
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"outputs": [],
@@ -937,6 +947,13 @@
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"- [Bash One-Liners Explained, Part III: All about redirections](http://www.catonmat.net/blog/bash-one-liners-explained-part-three/)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Exercise Break! (See below)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"heading_collapsed": true
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},
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"metadata": {},
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"source": [
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"#### Resources and More\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"heading_collapsed": true
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},
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"metadata": {},
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"source": [
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"#### Resources and More\n",
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"\n",
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"source": [
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"```sh\n",
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"# Create bash script\n",
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"echo \"#!/usr/bin/env bash\n",
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"echo '#!/usr/bin/env bash\n",
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"\n",
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"head -n 1 ../README.md\n",
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"\n",
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"if [[ $? -eq 0 ]]; then\n",
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" echo 'Successfully read beginning of file'; exit 0\n",
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" echo \"Successfully read beginning of file\"; exit 0\n",
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"else\n",
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" echo 'Failed to read beginning of file'; exit 1\n",
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"fi\" > test_exit_codes.sh\n",
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" echo \"Failed to read beginning of file\"; exit 1\n",
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"fi' > test_exit_codes.sh\n",
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"\n",
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"# Run bash script from above\n",
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"bash test_exit_codes.sh\n",
@@ -1826,6 +1839,13 @@
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"- [Unix / Linux: sftp File From One Server To Another](https://www.cyberciti.biz/faq/sftp-file-from-server-to-another-in-unix-linux/)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Exercise Break! (See below)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"all : file1_count.txt file2_count.txt file3_count.txt\n",
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"\n",
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"create :\n",
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" echo -e \"1\\n2\\n3\\n4\\n5\\n6\" > file1.txt\n",
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" echo -e \"Hello, world!\" > file2.txt\n",
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" echo -e \"We're learning bash programming!\" > file3.txt\n",
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" echo -e '1\\n2\\n3\\n4\\n5\\n6' > file1.txt\n",
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" echo -e 'Hello, world!' > file2.txt\n",
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" echo -e 'We're learning bash programming!' > file3.txt\n",
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"\n",
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"%_count.txt : %.txt\n",
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" wc $< > $@\n",
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"## Exercises"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"\n",
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"### Exercise 2 Download Data and Chop It Up\n",
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"\n",
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"Create a bash script to download the processed Long Beach V.A. data `processed.va.data` from the [Heart Disease Data Set](https://archive.ics.uci.edu/ml/datasets/Heart+Disease)and filter out for just subjects with Class 0 (last column). Save this subset of the data to a separate file.\n",
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"Create a bash script to download the processed Long Beach V.A. data `processed.va.data` from the [Heart Disease Data Set](https://archive.ics.uci.edu/ml/datasets/Heart+Disease)and filter out for just subjects with Class 0 (last column). Save this subset of the data to a separate file.\n",
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"\n",
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"The data can be found [here](https://archive.ics.uci.edu/ml/machine-learning-databases/heart-disease/).\n",
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"\n",
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"**Hint**: Use `wget`/`curl` to download file and `awk` to subset data.\n",
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"\n",
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"### Exercise 3 Search for Codons\n",
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"\n",
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"Using the random DNA sequence Python script from Exercise 1, generate a random sequence of DNA and count the number of times the DNA sequence \"TAA\" (a stop codon).\n",
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"\n",
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"**Hint**: Use `grep` to count number of occurrences. You can use the `-c` flag for `grep` to count things.\n",
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"\n",
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"**Bonus**: Simultaneously find all three stop codons: \"TAA\", \"TAG\", \"TGA\" and count them each."
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]
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},

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