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Merge pull request #1 from UUDeCART/master #3

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95e65c4
Merge pull request #1 from UUDeCART/master
mdsung Jun 28, 2019
7bbce9f
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mdsung Jun 28, 2019
e7e1dd8
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mdsung Jun 28, 2019
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1 change: 1 addition & 0 deletions .gitignore
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.gitattributes
__pycache__
*.swp
*.ziggy
2 changes: 1 addition & 1 deletion modules/module1/InClass/Index.ipynb
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Expand Up @@ -54,7 +54,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
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16 changes: 9 additions & 7 deletions modules/module1/InClass/environment_variables.ipynb
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Expand Up @@ -31,6 +31,7 @@
"outputs": [],
"source": [
"%%bash\n",
"\n",
"echo $HOME\n",
"echo $PATH"
]
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"outputs": [],
"source": [
"%%bash\n",
"rm -r /home/jovyan/bin\n",
"mkdir /home/jovyan/bin\n",
"cp ./ls /home/jovyan/bin/.\n",
"chmod +x /home/jovyan/bin/ls"
"rm -r /home/mdsung/bin\n",
"mkdir /home/mdsung/bin\n",
"cp ./ls /home/mdsung/bin/.\n",
"chmod +x /home/mdsung/bin/ls"
]
},
{
Expand All @@ -252,7 +253,8 @@
"outputs": [],
"source": [
"%%bash\n",
"/home/jovyan/bin/ls"
"pwd\n",
"/home/mdsung/bin/ls"
]
},
{
Expand Down Expand Up @@ -295,7 +297,7 @@
"echo $PATH\n",
"export PATH=$PATH:/home/jovyan/bin\n",
"which ls\n",
"ls /home/jovyan/DATA/Misc\n"
"ls /home/mdsung/DATA/Misc\n"
]
},
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
"version": "3.7.3"
}
},
"nbformat": 4,
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69 changes: 38 additions & 31 deletions modules/module1/InClass/finding_files.ipynb
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Expand Up @@ -81,17 +81,6 @@
"If I do not provide any expressions, all files under the specified print will be found."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"\n",
"find . "
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -128,7 +117,7 @@
"outputs": [],
"source": [
"%%bash\n",
"find /home/jovyan -name 'README'"
"find /home/mdsung -name 'README'"
]
},
{
Expand Down Expand Up @@ -172,7 +161,7 @@
"outputs": [],
"source": [
"%%bash\n",
"find /home/jovyan/work/decart_bootcamp_part1 -name '*.ipynb'\n"
"find /home/mdsung/2019_linux_bootcamp -name '*.ipynb'\n"
]
},
{
Expand All @@ -190,7 +179,7 @@
"source": [
"## Exercise\n",
"\n",
"In the /home/jovyan/DATA directory there are [WAVE files](https://en.wikipedia.org/wiki/WAV) (.wav) that are recordings of various heart anomalies. There are two types of Mitral valve problems: mitral stenosis (ms) and mitral regurgitation (mr). Use find with wildcards to find all the \"ms\" and \"mr\" WAVE files. Make sure that you do not match other files, for example pulmonary stenosis (ps). How many mitral WAVE files are there? How many WAVE files are there?"
"In the /home/mdsung/DATA directory there are [WAVE files](https://en.wikipedia.org/wiki/WAV) (.wav) that are recordings of various heart anomalies. There are two types of Mitral valve problems: mitral stenosis (ms) and mitral regurgitation (mr). Use find with wildcards to find all the \"ms\" and \"mr\" WAVE files. Make sure that you do not match other files, for example pulmonary stenosis (ps). How many mitral WAVE files are there? How many WAVE files are there?"
]
},
{
Expand All @@ -199,7 +188,8 @@
"metadata": {},
"outputs": [],
"source": [
"%%bash\n"
"%%bash\n",
"find /home/mdsung/DATA -name '*ms*.*'"
]
},
{
Expand All @@ -208,7 +198,8 @@
"metadata": {},
"outputs": [],
"source": [
"mitral_files()"
"%%bash\n",
"find /home/mdsung/DATA -name '*mr*.*'"
]
},
{
Expand All @@ -217,7 +208,16 @@
"metadata": {},
"outputs": [],
"source": [
"wave_files()"
"mitral_files(2)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"wave_files(11)"
]
},
{
Expand Down Expand Up @@ -258,7 +258,8 @@
"metadata": {},
"outputs": [],
"source": [
"%%bash"
"%%bash\n",
"find ~/DATA -size 10000 -name '*.txt'"
]
},
{
Expand All @@ -267,7 +268,7 @@
"metadata": {},
"outputs": [],
"source": [
"find_10k_files()"
"find_10k_files(66)"
]
},
{
Expand Down Expand Up @@ -317,7 +318,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep chapel /home/jovyan/DATA/Misc/obits.txt"
"grep chapel /home/mdsung/DATA/Misc/obits.txt"
]
},
{
Expand All @@ -334,7 +335,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i chapel /home/jovyan/DATA/Misc/obits.txt"
"grep -i chapel /home/mdsung/DATA/Misc/obits.txt"
]
},
{
Expand All @@ -351,7 +352,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i -c chapel /home/jovyan/DATA/Misc/obits.txt"
"grep -i -c chapel /home/mdsung/DATA/Misc/obits.txt"
]
},
{
Expand All @@ -368,7 +369,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i -c -r chapel /home/jovyan/DATA/Misc"
"grep -i -c -r chapel /home/mdsung/DATA/Misc"
]
},
{
Expand All @@ -385,7 +386,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i -l -r chapel /home/jovyan/DATA/Misc"
"grep -i -l -r chapel /home/mdsung/DATA/Misc"
]
},
{
Expand All @@ -402,8 +403,8 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i chapel /home/jovyan/DATA/Misc/obits.txt \\\n",
"/home/jovyan/DATA/Misc/icd9-short.txt"
"grep -i chapel /home/mdsung/DATA/Misc/obits.txt \\\n",
"/home/mdsung/DATA/Misc/icd9-short.txt"
]
},
{
Expand All @@ -413,7 +414,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i chapel /home/jovyan/DATA/Misc/*.txt"
"grep -i chapel /home/mdsung/DATA/Misc/*.txt"
]
},
{
Expand All @@ -434,7 +435,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep '7.-year-old' /home/jovyan/DATA/Misc/*.txt"
"grep '7.-year-old' /home/mdsung/DATA/Misc/*.txt"
]
},
{
Expand All @@ -458,15 +459,21 @@
"metadata": {},
"outputs": [],
"source": [
"bp_hr_ge200()"
"cd /home/mdsung/DATA/Numerics/mimic2/hr/subjects\n",
"grep -lrP \"\\b(?<!\\.)[23]\\d{2,2}\\b\" . > ~/hr200.txt ##\\b : word boundary \n",
"cd /home/mdsung/DATA/Numerics/mimic2/bp/subjects\n",
"grep -lrP \"\\b(?<!\\.)[23]\\d{2,2}\\b\" . > ~/bp200.txt\n",
"grep -Fx -f ~/bp200.txt ~/hr200.txt"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
"source": [
"bp_hr_ge200()"
]
}
],
"metadata": {
Expand All @@ -485,7 +492,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
"version": "3.7.3"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion modules/module1/InClass/introducing_shells.ipynb
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Expand Up @@ -86,7 +86,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
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