Python and Perl

1
Python and Perl

• Lecture 2
• Regular Expressions

2
Why use Regular Expressions?

• It is very powerful when extracting information
  from flat files.
• Easy to identify text rows with interesting data.
• Easy to retrieve sub groups/sub strings from text
  rows.
• Easy to identify numbers, words, white spaces and
  separators.

3
Real World exempel
ID TRBG361 standard mRNA PLN 1859
BP. XX AC X56734 S46826
Regular expression /ID/
Regular expression /AC\s\w/
4
Meta characters - 1

• Ordinary characters match them selves (a vs
  a, H vs H, Arsenal vs Arsenal).
• Meta characters are special characters that
  controls how other characters are interpreted.
• . Matches any characters (except newline \n)
  
• The characters that follows must match
  the first characters on a line/string.
• The characters before must match the last
  characters in the row/string.
• The character before matches zero or
  many occurrences.
• The character before matches one or
  many occurrences.
• ? The character before ? will match but is
  not necessary. (optional)

5
Meta characters - 2

• The characters preceding n , will
  match n repeats (an intervall like a2,4
  matches aa, aaa, aaaa).
• Characters enclosed like xyz , matches
  either one of x, y, z.
• Characters on either side like x y,
  matches x or y.
• () Characters enclosed by (), like
  ab(xyz)cd, determines a sub group xyz in the
  match.
• \ Meta characters preceded by \, matches
  themselves and revokes the meaning of the
  special meta feature. Like \ match plus sign.

6
Special Sequences

• \d Matches any number, same as 0-9.
• \D Inversed form of \d, matches any non
  number.
• \s Matches any white spaces, same as
  \t\n\r\f\v\b.
• \S Inversed form of \s, matches any non white
  space character
• \w Matches any alphanumeric character, same as
  a-zA-Z0-9_.
• \W Inversed form of \w.

7
How to apply RE? - overview

• Python
• Compile a pattern
• gt returns a re object.
• reobj re.compile(pattern)
• match the re object with a stringvariable.
• gt returns a match object.
• mobj reobj.match(stringvar)
• Test the match object
• if mobj
• Code block for match
• else
• Code block for non-match

• Perl
• Use the string operator
• string m/pattern/
• gt returns True if matching was succesful.
• example
• if ( string m/pattern/ )
• code block for match

See Lecture 1, example 7 for a complete program
using Reg Exp.
8
How to apply RE with sub groups? - overview

• Python
• Compile a pattern with subgroups like
  patt(sub1)er(sub2)n
• gt compile returns a re object.
• reobj re.compile(p(sub1)a(sub2)t)
• match the re object with a stringvariable.
• gt match/search returns a match object.
• mobj reobj.match(stringvar)
• Test the match object
• if mobj
• Extract sub groups
• subgr1 mobj.group(1)
• subgr2 mobj.group(2)

• Perl
• Use the string operator
• if ( stringm/p(sub1)a(sub2)t/)
• subgr1 1
• subgr2 2
• 1, 2, etc is built in variables in Perl. They
  are empty until a match was succesful.

import re racc re.compile(KW\s(.)\s(.))
m racc.match(line) if m subgr1
m.group(1) subgr2 m.group(2)
9
How does the syntax looks like?
My RE Perl program Filename RE.pl line
AC M5032 if ( line m/AC\s\w/
) print Found a match\n else print No
match found\n
My RE Python program Filename RE.py import
re line AC M50362 racc
re.compile(AC\s\w) if racc.match(line) pri
nt Found a match else print No match found