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Update for MSc course
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‎Files/humchrx.txt

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‎Intro-to-Python/00.ipynb

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"* [01](Intro-to-Python/01.ipynb) Basic data types and operations (numbers, strings) \n",
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"\n",
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"### Session 2\n",
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"* [02](Intro-to-Python/02.ipynb) String manipulation \n",
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"* [02](02.ipynb) String manipulation \n",
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"* [03](Intro-to-Python/03.ipynb) Data structures: Lists and Tuples\n",
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"* [04](Intro-to-Python/04.ipynb) Data structures (continued): dictionaries\n",
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"\n",
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"### Session 3\n",
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"* [05](Intro-to-Python/05.ipynb) Control statements: if, for, while, try statements\n",
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"* [06](Intro-to-Python/06.ipynb) Functions\n",
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"* [07](Intro-to-Python/07.ipynb) Scripting with python\n",
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"* [07](Intro-to-Python/07.ipynb) Files, Scripting and Modules\n",
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"* [08](Intro-to-Python/08.ipynb) Data Analysis and plotting with Pandas\n",
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"* [09](Intro-to-Python/09.ipynb) Reproducible Bioinformatics Research\n",
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"\n",
@@ -171,7 +171,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎Intro-to-Python/01.ipynb

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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"What is your name?\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"'Caleb'"
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"''"
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]
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},
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"execution_count": 7,
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ACGTATAGCA\n"
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"Please Enter a DNA sequence: \n",
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"\n"
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]
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}
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],
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"wxtylkas\n"
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"Please Enter aa sequence: \n",
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"\n"
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]
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}
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],
@@ -263,7 +272,7 @@
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"Welcome to Python 3.6's help utility!\n",
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"\n",
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"If this is your first time using Python, you should definitely check out\n",
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"the tutorial on the Internet at https://docs.python.org/3.6/tutorial/.\n",
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"the tutorial on the Internet at http://docs.python.org/3.6/tutorial/.\n",
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"\n",
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"Enter the name of any module, keyword, or topic to get help on writing\n",
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"Python programs and using Python modules. To quit this help utility and\n",
@@ -274,18 +283,7 @@
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"with a one-line summary of what it does; to list the modules whose name\n",
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"or summary contain a given string such as \"spam\", type \"modules spam\".\n",
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"\n",
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"Help on built-in function print in module builtins:\n",
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"\n",
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"print(...)\n",
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" print(value, ..., sep=' ', end='\\n', file=sys.stdout, flush=False)\n",
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" \n",
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" Prints the values to a stream, or to sys.stdout by default.\n",
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" Optional keyword arguments:\n",
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" file: a file-like object (stream); defaults to the current sys.stdout.\n",
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" sep: string inserted between values, default a space.\n",
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" end: string appended after the last value, default a newline.\n",
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" flush: whether to forcibly flush the stream.\n",
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"\n",
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"help> \n",
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"\n",
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"You are now leaving help and returning to the Python interpreter.\n",
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"If you want to ask for help on a particular object directly from the\n",
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"execution_count": 11,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Enter your name: \n"
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]
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},
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{
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"data": {
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"text/plain": [
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"'Caleb'"
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"''"
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]
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},
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"execution_count": 11,
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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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"execution_count": 35,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"True"
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]
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},
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"execution_count": 35,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"z = 2\n",
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"z == 2"
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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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"execution_count": 36,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"False"
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]
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},
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"execution_count": 36,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"z > 2"
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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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"execution_count": 37,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"False"
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]
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},
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"execution_count": 37,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"0.5 < z <= 1"
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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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"execution_count": 38,
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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": "code",
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"execution_count": null,
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"execution_count": 39,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"True"
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]
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},
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"execution_count": 39,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"# we can check if a given motif is in sequence\n",
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"\n",
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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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"execution_count": 40,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"True"
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]
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},
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"execution_count": 40,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"# We can also check if a given motif is absent\n",
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"\n",
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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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"execution_count": 41,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'ATTAAGGCTGTT'"
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]
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},
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"execution_count": 41,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"#we can concatentate two strings\n",
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"\n",
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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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"execution_count": 42,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'GGCTGTTGGCTGTTGGCTGTTGGCTGTT'"
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]
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},
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"execution_count": 42,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"# Create a long string from a substring by multiplying with an integer\n",
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"'GGCTGTT' * 4"
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"source": [
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"We'll continue with string formatting in the next lecture. "
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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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"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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"metadata": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

‎Intro-to-Python/02.ipynb

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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

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