Python Input/Output

class: center, middle

# Python 3: Data Input and output

---
      #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
      ```