Python Input/Output

class: center, middle

# Python 2: Loops & Data Input and output

---
      # Python function refresher

There are many python functions. We will use a few in this section. Reminder that documentation is available here.

[https://docs.python.org/3/library/functions.html](https://docs.python.org/3/library/functions.html)
      
      ---
      # Logic in program flow

Need to be able to specify logic

```python
      if TRUE:
          THEN DO X
      elif OTHER_THING_TRUE:
          THEN DO Y 
      else:
          THEN DO Z
      ```

And Loops
      ```python
      while ( TRUE ):
          Do X

for ITERATOR in LIST:
          Do Y
      for i in range(5):
          print(i) 
      ```
      ---
      # Python uses indentation

* Python uses indentation to indicate the branching in the logic.

.center[![cyoa](images/deadwood.jpg "Choose your Own Adventure")]
      
      This indentation can be either spaces or tabs. Emacs/Atom/Vi
      allow customizing your editor so that when [tab] is typed it
      will either insert 4 spaces or a tab. Switching between editors while editing a file can sometimes cause problems.

Solution: delete the indendentation and enter the tab (or spaces) again.
      
      After this slide you will now understand this scene from [Silicon Valley](https://www.youtube.com/watch?v=SsoOG6ZeyUI).

---
      # Logical operators

* `===` for equality. Returns true if two values are equal. Do not use `=` which is assignment
      ```python
      x=10
      if x == 10:
          print("this is a ten")
      ```      
      * `!=` for not equal. 
      
      * `<` - less than `>` - greater than `<=` less than or equal to `>=` greater than or equal to
      ```python
      a = 7
      b = 82
      if b > a:
          print("b is greater than a")
      ```
      ---
      # Other operators

* `is` - tests for the content of the string being the same

```python
      a="fiat"
      b="".join(['f','i','a','t'])
      if a is b:
         print("strings are same")
      if a == b:
         print("these are the same string: %s %s"%(a,b))    
      ```
      ---
      #Logical operators to combine or modify statements

* Not - `not` 
      * Or - `or` 
      * And - `and`

```python
      a=10
      b=12
      c=13
      if a < b and b < c:
          print("a is smaller than c")
      ```

```python
      if not a == b:
          print("a is not equal to b")
      else:
         print("a is equal to b")
      ```
      ---
      #Loops

* while loops run as long as condition is true
      ```python
      x=1
      while( x < 10 ):
          print("x is",x)
          x += 1
      ```
      * for loops loop through a set of items
      ```python
      DNA="AAAGCCAAG"
      for base in DNA:
          print("base is %s"%(base))
      ```

---
      #Python range operator

Simple way to setup a counter. See the [range](https://docs.python.org/3/library/functions.html#func-range) function

```python
      for i in range(1,10): # forwards counting
          print(i)
      for i in range(10,0,-1): #backwards counting
          print(i)
      for i in range(2,16,2): # count by twos
          print(i)
      ```
      ---
      #Loop on a list

Iterate on a list using indexes
      ```python
      list = (7, 10, 2, 2, 7)
      for i in range(len(list)):
          print("list[%d] = %s"%(i,list[i]))
      ```
      Iterate on a list directly
      ```python
      for item in list:
         print("item is",item)
      ```
      
      ---
      # Exiting the loop

* the `break` function stops a loop and exits it

* the `continue` stops executing in the loop and starts back at top

```python
      list = ('a', 'b', 'c', 'd')
      for l in list:
          if l == "b":
              continue
          print(l)
      ```
      ```
      a
      c
      d
      ```
      
      ---
      #File handles / Data streams

The `open` function is used to open file handles. Good reference
      can be found at
      https://en.wikibooks.org/wiki/Python_Programming/Input_and_Output

Data streams could be from cmdline (eg STDIN)
      ```shell
      $ cat file | python myscript.py```

Can also be a file
      ```python
      filehandle = open(myfile,"r")```

---
      # Getting data into your program

`open` - is for opening a file

There are two arguments, one is the filename, the other is how
      to open, reading, writing. For text data use "r" but if binary
      data use "rb". 
      
      ```python
      file = "data1.dat"
      fh = open(file,"r")
      for line in fh:
          print(line)
      ```

---
      #Alternative structure for opening

This will throw a warning if the file cannot be opened

```python
      with open(myfile,"r") as fh:
          for line in fh:
              print(line)
      ```
      ---
      #Writing data

Write data or text to a file.
      
      ```python
      ofh = open("my_data.tab","w")
      ofh.write("Species\tHabitat\tSize\n")
      ofh.write("Crab\tBeach\tM\n")
      ofh.write("Fish\tOcean\tS\n")
      ```
      ```shell
      $ cat my_data.tab
      Species	Habitat	Size
      Crab	Beach	M
      Fish	Ocean	S
      ```
     
      ---
      #Modules/Libraries/Packages

Modules are collections of code routines. We will talk more
      about functions/routines in next lecture. Can use these as
      tools.

* [sys](https://docs.python.org/3/library/sys.html) - System-specific parameters and functions
      * [urllib.request](https://docs.python.org/3/library/urllib.request.html#module-urllib.request) - URLs for opening web or network connections
      * [csv](https://docs.python.org/3/library/csv.html) - Comma and
      Tab delimited data parsing

---
      #Reading in STDIN

Remember we can pass data into a program via STDIN if we use the
      '|' "pipes" in UNIX

```python
      import sys

counter = 0
      for line in sys.stdin:
          counter += 1
      print ("There are",counter, "lines")
      ```
      ---
      #Data streams don't have to be files

Can be a network connection (eg URL for web or FTP)
      ```python
      import urllib.request
      orginfo = "https://biodataprog.github.io/programming-intro/data/random_exons.csv"
      info = urllib.request.urlopen(orginfo)
      for line in info:
          linestrip = line.decode('UTF-8').strip()
          print(linestrip)
      ```
      ---
      #CSV module

```python
      import csv

file2 = "test2.csv"
      with open(file2) as csvfile:
          reader = csv.reader(csvfile,delimiter=",",quotechar='|')
          for row in reader:
              print("\t".join(row))

with open("outtest.csv","w") as csvfile:
          writer = csv.writer(csvfile,delimiter="\t")
          writer.writerow(["Name","Flavor","Color"])
          writer.writerow(["Apple","Sweet","Red"])
          writer.writerow(["Pretzel","Salty","Brown"])      ```
      
      ---
      #command line arguments

* import sys
      * get the command line input as a list from sys.argv[]

```bash
      $ python argparse.py arg1 arg2 arg3 this-is-one "this is one"
      ```
      ```python
      import sys
      for n in range(len(sys.argv)):
          printf 'argv[%d] = %s' %(n, sys.argv[n])    
      ```
      
      ```text
      argv[0] = argparse.py
      argv[1] = arg1
      argv[2] = arg2
      argv[3] = arg3
      argv[4] = this-is-one
      argv[5] = this is one
      ```