Processing regular expressions from a file

An example from StackOverflow

Introductory Topics

• The Hello World Program
• Solving Quadratic Equations
  quad1.pl prompts the user for input values, uses chop() to delete the new line characters, solve the quadratic equation using (-b +- sqrt(b^2-4ac))/2a and prints out the two roots.
  The isn't any error checking in this version. This provides examples of :
  1. Prompting the user for integer values, storing values in variables
  2. Using integer values in calculations
  3. Displaying messages to users that include values from variables
• Example: How to read a text file into an array and print out the array.
• Reference: A good list of Perl Tutorials and web sites for learning Perl.

Regular Expressions

• Reading regular expressions from a file

References/Files

GFF3 Format and CRISPRs
• how to convert blast to gff3
• cnv_blast2gff.pl
• sequenceontology.org/gff3Generic Feature Format Version 3
• gmod.org
• CRISPRs and epigenome editing at Nature.com
• CRISPR at addgene.org
• crispr.u-psud.fr/
• CRISPR Genome Engineering Resources at www.genome-engineering.org/crispr

perl
• String matching
• String matching examples
• A word can be split into characters, a sentence split into words and a paragraph split into sentences:
  • @chars = split(//, $word);
  • @words = split(/ /, $sentence);
  • @sentences = split(/\./, $paragraph);
  • In the first case the null string is matched between each character, and that is why the @chars array is an array of characters - ie an array of strings of length 1.

Directory list for ./

Directory:	ProjectNotes_files
filename:	Beginning Perl for Bioinformatics.pdf
filename:	FinalProject.pdf
filename:	Module11DynamicProgramingandHeuristics.pdf
filename:	ProjectNotes.htm
filename:	Reference_D-fkty.pdf
filename:	helloWorld.php
filename:	parms.html
filename:	quad1.pl
filename:	quad1.txt
filename:	reverse_str.html
filename:	string1-pl.html
filename:	strs.html
filename:	test.dat
filename:	uniqueKmersEndingGG.txt
filename:	~$ojectNotes.htm

Notes

• Install Apache Web server and MysQL XAMPP

• PHP tutorials and test-it-out environment w3Schools.com

• JaveScript tutorials and test-it-out environment w3Schools.com

  Web server http.txt conf