Regex practice

Online resources

good tutorial on using regex: http://regexone.com/lesson/introduction_abcs
testing page for regex: https://regex101.com/#

Setup

Below is the code to get you setup. You can copy and paste these dataframes into your code to create the dataframes you will need.

library(dplyr)

# Note that I'm using data_frame() from the dplyr package to make my data.frame!
counties <- data_frame(counties = c('MA, 25, 001, Barnstable County, H1', 
              'MA, 25, 003, Berkshire County, H4', 
              'MA, 25, 005, Bristol County, H1',
              'MA, 25, 007, Dukes County, H1',
              'MA, 25, 009, Essex County, H4',
              'MA, 25, 011, Franklin County, H4',
              'MA, 25, 013, Hampden County, H4',
              'MA, 25, 015, Hampshire County, H4',
              'MA, 25, 017, Middlesex County, H4',
              'MA, 25, 019, Nantucket County, H4',
              'MA, 25, 021, Norfolk County, H1',
              'MA, 25, 023, Plymouth County, H1',
              'MA, 25, 025, Suffolk County, H4',
              'MA, 25, 027, Worcester County, H4', 
              'VA, 51, 193, Westmoreland County, H1',
              'VA, 51, 195, Wise County, H1',
              'VA, 51, 197, Wythe County, H1',
              'VA, 51, 199, York County, H1',
              'VA, 51, 510, Alexandria city, C7',
              'VA, 51, 515, Bedford city, C7',
              'VA, 51, 520, Bristol city, C7',
              'VA, 51, 530, Buena Vista city, C7',
              'VA, 51, 540, Charlottesville city, C7',
              'VA, 51, 550, Chesapeake city, C7',
              'VA, 51, 570, Colonial Heights city, C7'
))

dna_seqs <- data_frame(seq =c('ATG CAA TGG GGA AAT GGT ACC AGG TCC GAA CTT AAT GAG GTA AGA CAG ATT TAA', 
'A TGC AAT GGG GAA ATG TTA CCA GGT CCG AAC TTA TTG AGG TAA GAC AGA TTT AA', 
'AT GCA ATG GGG AAA TGT TAC CAG GTC CGA ACT TAT TAA GGT AAG ACA GAT TTA A'))

Questions

Using grepl and filter select the massachusetts counties that contain the letter ‘h’ in their county name.
Using grepl and filter select the massachusetts counties that contain the number 2 in their three digit county code.
Using gsub, remove the word ‘County’ or ‘city’ and the trailing white space after the county name.
Open reading frames (ORF) are sections of DNA that have the potential to code for a peptide/protein. They occur between a start codon ATG and a stop codon (TAA, TAG, or TGA) on the DNA. Write the regular expression that selects the ORF of the DNA sequences provided.

Bonus questions 5. Super challenge: 272_71.9333_33.9167 and 80.9_-161.533 are the latitude and longitude separated by an underscore. Can you write a regular expression that highlights the latitude and longitude?

For number 4, use R to extract the open reading frames into a new vector/dataframe.