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PYTHON II
Good book can help but:
	Un-recommendation: Zelle python book


Scripts -- if you start with examples in the scripts folder, 
you won't be able to make a new one and edit it, so we 
will eventually rename the examples as 1,2,3

Exponents: ** not ^

.strip() -- if you specify \n, your program might not work cross platform
if you know there won't be empty fields, you can use .strip() or 
you can do both .strip{"\n").strip("\r")

List indexing -- why [::-1] reverses a string or list

Computer friendly data files:
** Example Nanodrop file .ndj in examples folder

Reading lines in python:
	to get the whole file in a list at once (needs memory), you can use 
	for Line in InFile.readlines():
	but usually more efficient to just do it line by line...
	for Line in InFile:
	
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Exercise: 
read fasta file into a list
(create in scripts folder, run from examples folder)

use FPexcerpt.fta as the input.

Outline:
1. Get name of file from user input (extra credit, make it do multiple files).
To start: get it to print the file name.


2. Use sys.stderr.write() to give feedback
   (Won't be captured by >)
   
3. Print help if the user doesn't enter a file name

4. open file, read in lines:
 (extra credit: skip blank, header, and comment lines)

5. if it is a sequence name, save it in a list, increment the sequence number. 
set up a blank sequence to go along with it

6. if it is a portion of a sequence, strip out [spaces, \n, dashes] and append to existing sequence

7. when done, use a new for loop to go through and print out a table of size, pct composition AGCT

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Potential class projects:

• Nanodrop data to XYYY (see ndj in examples folder)
	skip blanks
• Extract fasta alignment from specified contig in specified .ace file
 	format: CO is the contig, RD are the reads that went into it.
 	see ace_output.fta and ace_example.ace, alongn with VM1
• Print formatted output using HTML with 
 <pre><code><span style="color: #0022FF">TEXT</span></code></pre>
  see color.html