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https://github.com/prog4biol/evop2018

Programming for Evolutionary Biology Python in 2 Days
https://github.com/prog4biol/evop2018
Last synced: about 1 month ago
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Programming for Evolutionary Biology Python in 2 Days
Host: GitHub
URL: https://github.com/prog4biol/evop2018
Owner: prog4biol
Created: 2018-02-28T20:18:10.000Z (almost 7 years ago)
Default Branch: master
Last Pushed: 2018-10-19T18:31:24.000Z (about 6 years ago)
Last Synced: 2024-08-02T11:22:14.240Z (4 months ago)
Language: Python
Size: 3.38 MB
Stars: 2
Watchers: 2
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
Awesome Lists containing this project

awesome-bacteria - evop2018 - Programming for Evolutionary Biology Python in 2 Days (2018). (Educational resources / Python)
README

        # Python for EVOP2018

### Sofia Robb  

[Lecture Material](EVOP_Python_2018.md) [[pdf](EVOP_Python_2018.pdf)] [[markdown](EVOP_Python_2018.md)]   

[Lecture Files](files)  

[Lecture Scripts](scripts)  

To download all files and scripts, run this command:  

`git clone https://github.com/prog4biol/evop2018.git`

Table of Contents

=================

   * [Python for EVOP 2018](EVOP_Python_2018.md/#python-for-evop-2018)

      * [Why Python?](EVOP_Python_2018.md/#why-python)

      * [Why Script?](EVOP_Python_2018.md/#why-script)

      * [Teaching Format](EVOP_Python_2018.md/#teaching-format)

      * [Installing Python](EVOP_Python_2018.md/#installing-python)

      * [Python References](EVOP_Python_2018.md/#python-references)

            * [Books](EVOP_Python_2018.md/#books)

            * [Websites](EVOP_Python_2018.md/#websites)

            * [Practice](EVOP_Python_2018.md/#practice)

      * [Python Overview](EVOP_Python_2018.md/#python-overview)

         * [Running Python](EVOP_Python_2018.md/#running-python)

            * [Interactive Interpretor](EVOP_Python_2018.md/#interactive-interpretor)

            * [Python Scripts](EVOP_Python_2018.md/#python-scripts)

            * [Running Python Scripts](EVOP_Python_2018.md/#running-python-scripts)

            * [A quicker/better way to run python scripts](EVOP_Python_2018.md/#a-quickerbetter-way-to-run-python-scripts)

         * [Syntax](EVOP_Python_2018.md/#syntax)

            * [Python Identifiers](EVOP_Python_2018.md/#python-identifiers)

            * [Naming conventions for Python Identifiers](EVOP_Python_2018.md/#naming-conventions-for-python-identifiers)

            * [Reserved Words](EVOP_Python_2018.md/#reserved-words)

            * [Lines and Indentation](EVOP_Python_2018.md/#lines-and-indentation)

            * [Comments](EVOP_Python_2018.md/#comments)

            * [Blank Lines](EVOP_Python_2018.md/#blank-lines)

         * [Data Types and Variables](EVOP_Python_2018.md/#data-types-and-variables)

            * [Numbers and Strings](EVOP_Python_2018.md/#numbers-and-strings)

            * [Lists](EVOP_Python_2018.md/#lists)

            * [Tuples](EVOP_Python_2018.md/#tuples)

            * [Dictionary](EVOP_Python_2018.md/#dictionary)

            * [Command line parameters: A Special Built-in List](EVOP_Python_2018.md/#command-line-parameters-a-special-built-in-list)

            * [What kind of object am I working with?](EVOP_Python_2018.md/#what-kind-of-object-am-i-working-with)

         * [Operators](EVOP_Python_2018.md/#operators)

            * [Arithmetic Operators](EVOP_Python_2018.md/#arithmetic-operators)

            * [Assignment Operators](EVOP_Python_2018.md/#assignment-operators)

            * [Comparison Operators](EVOP_Python_2018.md/#comparison-operators)

            * [Logical Operators](EVOP_Python_2018.md/#logical-operators)

            * [Membership Operators](EVOP_Python_2018.md/#membership-operators)

            * [Operator Precedence](EVOP_Python_2018.md/#operator-precedence)

         * [Truth](EVOP_Python_2018.md/#truth)

            * [Test for truth](EVOP_Python_2018.md/#test-for-truth)

         * [Logic: Control Statements](EVOP_Python_2018.md/#logic-control-statements)

            * [If Statement](EVOP_Python_2018.md/#if-statement)

            * [if/elif](EVOP_Python_2018.md/#ifelif)

         * [Numbers](EVOP_Python_2018.md/#numbers)

            * [integer](EVOP_Python_2018.md/#integer)

            * [floating point number](EVOP_Python_2018.md/#floating-point-number)

            * [complex number](EVOP_Python_2018.md/#complex-number)

            * [Conversion functions](EVOP_Python_2018.md/#conversion-functions)

            * [Numeric Functions](EVOP_Python_2018.md/#numeric-functions)

         * [Comparing two numbers](EVOP_Python_2018.md/#comparing-two-numbers)

         * [Sequences](EVOP_Python_2018.md/#sequences)

            * [Strings](EVOP_Python_2018.md/#strings)

               * [Quotation Marks](EVOP_Python_2018.md/#quotation-marks)

               * [Strings and the print() function](EVOP_Python_2018.md/#strings-and-the-print-function)

               * [Special/Escape Characters](EVOP_Python_2018.md/#specialescape-characters)

               * [Concatenation](EVOP_Python_2018.md/#concatenation)

               * [The difference between string   and integer  ](EVOP_Python_2018.md/#the-difference-between-string--and-integer-)

               * [Determine the length of a string](EVOP_Python_2018.md/#determine-the-length-of-a-string)

               * [Changing String Case](EVOP_Python_2018.md/#changing-string-case)

               * [Find and Count](EVOP_Python_2018.md/#find-and-count)

               * [Find and Replace](EVOP_Python_2018.md/#find-and-replace)

               * [Extracting a Substring, or Slicing](EVOP_Python_2018.md/#extracting-a-substring-or-slicing)

               * [Locate and Report](EVOP_Python_2018.md/#locate-and-report)

               * [Other String Methods](EVOP_Python_2018.md/#other-string-methods)

            * [String Formatting](EVOP_Python_2018.md/#string-formatting)

            * [Lists and Tuples](EVOP_Python_2018.md/#lists-and-tuples)

               * [Lists](EVOP_Python_2018.md/#lists-1)

               * [Tuples](EVOP_Python_2018.md/#tuples-1)

               * [Back to Lists](EVOP_Python_2018.md/#back-to-lists)

               * [Accessing Values in Lists](EVOP_Python_2018.md/#accessing-values-in-lists)

               * [Changing Values in a List](EVOP_Python_2018.md/#changing-values-in-a-list)

               * [Extracting a Subset of a List, or Slicing](EVOP_Python_2018.md/#extracting-a-subset-of-a-list-or-slicing)

               * [List Operators](EVOP_Python_2018.md/#list-operators)

               * [List Functions](EVOP_Python_2018.md/#list-functions)

               * [List Methods](EVOP_Python_2018.md/#list-methods)

               * [Building a List one Value at a Time](EVOP_Python_2018.md/#building-a-list-one-value-at-a-time)

         * [Loops](EVOP_Python_2018.md/#loops)

            * [While loop](EVOP_Python_2018.md/#while-loop)

               * [While Loop Syntax](EVOP_Python_2018.md/#while-loop-syntax)

               * [Infinite Loops](EVOP_Python_2018.md/#infinite-loops)

            * [For Loops](EVOP_Python_2018.md/#for-loops)

               * [For Loop Syntax](EVOP_Python_2018.md/#for-loop-syntax)

            * [Loop Control](EVOP_Python_2018.md/#loop-control)

               * [Loop Control: Break](EVOP_Python_2018.md/#loop-control-break)

               * [Loop Control: Continue](EVOP_Python_2018.md/#loop-control-continue)

            * [Iterators](EVOP_Python_2018.md/#iterators)

            * [List Comprehension](EVOP_Python_2018.md/#list-comprehension)

         * [Dictionaries](EVOP_Python_2018.md/#dictionaries)

            * [Creating a Dictionary](EVOP_Python_2018.md/#creating-a-dictionary)

            * [Accessing Values in Dictionaries](EVOP_Python_2018.md/#accessing-values-in-dictionaries)

            * [Changing Values in a Dictionary](EVOP_Python_2018.md/#changing-values-in-a-dictionary)

            * [Accessing Each Dictionary Key/Value](EVOP_Python_2018.md/#accessing-each-dictionary-keyvalue)

            * [Building a Dictionary one Key/Value at a Time](EVOP_Python_2018.md/#building-a-dictionary-one-keyvalue-at-a-time)

            * [Checking That Dictionary Keys Exist](EVOP_Python_2018.md/#checking-that-dictionary-keys-exist)

            * [Dictionary Operators](EVOP_Python_2018.md/#dictionary-operators)

            * [Sorting Dictionary Keys](EVOP_Python_2018.md/#sorting-dictionary-keys)

            * [Dictionary Functions](EVOP_Python_2018.md/#dictionary-functions)

            * [Dictionary Methods](EVOP_Python_2018.md/#dictionary-methods)

         * [Sets](EVOP_Python_2018.md/#sets)

            * [Set Operators](EVOP_Python_2018.md/#set-operators)

               * [Difference](EVOP_Python_2018.md/#difference)

               * [Union](EVOP_Python_2018.md/#union)

               * [Intersection](EVOP_Python_2018.md/#intersection)

               * [Symmetric Difference](EVOP_Python_2018.md/#symmetric-difference)

            * [Set Functions](EVOP_Python_2018.md/#set-functions)

            * [Set Methods](EVOP_Python_2018.md/#set-methods)

         * [I/O and Files](EVOP_Python_2018.md/#io-and-files)

            * [Writing to the Screen](EVOP_Python_2018.md/#writing-to-the-screen)

            * [Reading input from the keyboard](EVOP_Python_2018.md/#reading-input-from-the-keyboard)

            * [Reading from a File](EVOP_Python_2018.md/#reading-from-a-file)

            * [Open a File](EVOP_Python_2018.md/#open-a-file)

            * [Reading the contents of a file](EVOP_Python_2018.md/#reading-the-contents-of-a-file)

            * [Opening a file with with open() as fh:](EVOP_Python_2018.md/#opening-a-file-with-with-open-as-fh)

            * [Writing to a File](EVOP_Python_2018.md/#writing-to-a-file)

            * [Building a Dictionary from a File](EVOP_Python_2018.md/#building-a-dictionary-from-a-file)

         * [Regular Expressions](EVOP_Python_2018.md/#regular-expressions)

            * [Individual Characters](EVOP_Python_2018.md/#individual-characters)

            * [Character Classes](EVOP_Python_2018.md/#character-classes)

            * [Anchors](EVOP_Python_2018.md/#anchors)

            * [Quantifiers](EVOP_Python_2018.md/#quantifiers)

            * [Variables and Patterns](EVOP_Python_2018.md/#variables-and-patterns)

            * [Either Or](EVOP_Python_2018.md/#either-or)

            * [Subpatterns](EVOP_Python_2018.md/#subpatterns)

            * [Using Subpatterns Inside the Regular Expression Match](EVOP_Python_2018.md/#using-subpatterns-inside-the-regular-expression-match)

            * [Using Subpatterns Outside the Regular Expression](EVOP_Python_2018.md/#using-subpatterns-outside-the-regular-expression)

            * [Get position of the subpattern with finditer()](EVOP_Python_2018.md/#get-position-of-the-subpattern-with-finditer)

            * [Subpatterns and Greediness](EVOP_Python_2018.md/#subpatterns-and-greediness)

            * [Practical Example: Codons](EVOP_Python_2018.md/#practical-example-codons)

            * [Truth and Regular Expression Matches](EVOP_Python_2018.md/#truth-and-regular-expression-matches)

            * [Using Regular expressions in substitutions](EVOP_Python_2018.md/#using-regular-expressions-in-substitutions)

            * [Using subpatterns in the replacement](EVOP_Python_2018.md/#using-subpatterns-in-the-replacement)

            * [Regular Expression Option Modifiers](EVOP_Python_2018.md/#regular-expression-option-modifiers)

         * [Basic FASTA Parser](EVOP_Python_2018.md/#basic-fasta-parser)

         * [Functions](EVOP_Python_2018.md/#functions)

            * [Defining a Function that calculates GC Content](EVOP_Python_2018.md/#defining-a-function-that-calculates-gc-content)

               * [Using your function to calculate GC content](EVOP_Python_2018.md/#using-your-function-to-calculate-gc-content)

               * [The details](EVOP_Python_2018.md/#the-details)

            * [Naming Arguments](EVOP_Python_2018.md/#naming-arguments)

            * [Keyword Arguments](EVOP_Python_2018.md/#keyword-arguments)

            * [Default Values for Arguments](EVOP_Python_2018.md/#default-values-for-arguments)

            * [Lambda expressions](EVOP_Python_2018.md/#lambda-expressions)

         * [Scope](EVOP_Python_2018.md/#scope)

            * [Global Variables](EVOP_Python_2018.md/#global-variables)

            * [Local Variables](EVOP_Python_2018.md/#local-variables)

            * [Global](EVOP_Python_2018.md/#global)

         * [Data Structures](EVOP_Python_2018.md/#data-structures)

            * [List of lists](EVOP_Python_2018.md/#list-of-lists)

            * [Lists of dictionaries](EVOP_Python_2018.md/#lists-of-dictionaries)

            * [Dictionaries of lists](EVOP_Python_2018.md/#dictionaries-of-lists)

            * [Dictionaries of dictionaries](EVOP_Python_2018.md/#dictionaries-of-dictionaries)

         * [Pipelines](EVOP_Python_2018.md/#pipelines)

            * [subprocess Module](EVOP_Python_2018.md/#subprocess-module)

            * [shell=True](EVOP_Python_2018.md/#shelltrue)

            * [Use Error Code to Control Pipeline](EVOP_Python_2018.md/#use-error-code-to-control-pipeline)

      * [Biopython](EVOP_Python_2018.md/#biopython)

         * [What is biopython?](EVOP_Python_2018.md/#what-is-biopython)

         * [Installing Biopython](EVOP_Python_2018.md/#installing-biopython)

         * [Biopython documentation](EVOP_Python_2018.md/#biopython-documentation)

         * [Working with DNA and protein sequences](EVOP_Python_2018.md/#working-with-dna-and-protein-sequences)

         * [From ... import ...](EVOP_Python_2018.md/#from--import-)

         * [Bio.Alphabets](EVOP_Python_2018.md/#bioalphabets)

         * [Extracting a subsequence](EVOP_Python_2018.md/#extracting-a-subsequence)

         * [Read a FASTA file](EVOP_Python_2018.md/#read-a-fasta-file)

         * [Convert fasta file to python dictionary in one line](EVOP_Python_2018.md/#convert-fasta-file-to-python-dictionary-in-one-line)

         * [Seq methods](EVOP_Python_2018.md/#seq-methods)

         * [SeqRecord objects](EVOP_Python_2018.md/#seqrecord-objects)

         * [Retrieving annotations from GenBank file](EVOP_Python_2018.md/#retrieving-annotations-from-genbank-file)

         * [File Format Conversions](EVOP_Python_2018.md/#file-format-conversions)

         * [Parsing BLAST output](EVOP_Python_2018.md/#parsing-blast-output)

         * [There are many other uses for Biopython](EVOP_Python_2018.md/#there-are-many-other-uses-for-biopython)

         * [Why use biopython](EVOP_Python_2018.md/#why-use-biopython)

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