Perl

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Perl 3 Regular Expressions

• Pattern Analysis in Biology

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Patterns in Biology

• Biology is all about patterns
• (Im working on a book)
• DNA patterns
• restriction sites
• promoters/transcription factor binding sites
• intron splice site
• Protein patterns
• conserved domains (motifs)
• active sites
• structural motifs (membrane spanning, signal
  peptide, etc.)

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Computers are good at finding Patterns

• Find command in your word processor, Find
  File in your computers operating system
• Based on an underlying concept called a Regular
  Expression (regexp)
• a regexp is a text string, such as aatcg
• can also have variable characters aatacg
• or a wildcard aaxcg
• or a variable spacer aax(1-20)cg

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grep

• grep is a handy Unix tool to get regular
  expresssions
• it is powerful and moderately complex tool (has
  one of the longest man pages in the online Unix
  help system)
• does not require its own OReilly book, but is a
  solid chapter in Intro and intermediate
  Unix/Linux books

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Perl Regular Expressions

• Perl Regular Expressions are more complex and
  more powerful than grep
• Can find and substitute bits of text in a single
  command
• Various options for fuzzy matches
• Perl regular expressions can get extremely
  complex - goes way beyond the scope of this
  course
• gt man perlrequick

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The Match Operator / /

• Perl uses a special type of operator to do text
  matching with regular expressions
• / /
• The symbol is a pattern match comparison
  operator
• - it can be translated as contains
• The forward slashes contain the pattern to be
  matched, like this
• print EcoRI site found! if dna /GAATTC/

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Alternative Characters

• Square brackets within the match expression allow
  for alternative characters
• if dna /GGGGATCCCC/
• This will match an DNA string that starts with
  GGG has G,A,T, or C in the 4th position,
  followed by CCC
• A vertical line within the /expression/ allows
  you to look for either of two completely
  different patterns
• if dna /GAATTCAAGCTT/

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Wildcards

• Perl has a set of wildcard characters for Reg.
  Exps. that are completely different than the ones
  used by Unix
• the dot (.) matches any character
• \d matches any digit (a number from 0-9)
• \w matches any text character (a letter
  or number, not punctuation or space)
• \s matches white space (any amount)
• matches the beginning of a line
• matches the end of a line
• (Yes, this is very confusing!)

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Repeat for a count

• Use curly brackets to show that a character
  repeats a specific number (or range) of times
• find an EcoRI fragment of 100-500 bp length (two
  EcoRI sites with any other sequence between)
• if ecofrag /GAATTCGATC100,500GAATTC/
• The sign is used to indicate an unlimited
  number of repeats (occurs 1 or more times)

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It gets worse

• What if you need to match text that contains a
  special character?
• (the dot shows up all the time in GenBank IDs,
  filenames, etc.)
• Now you have to use a backslash (\) to escape
  the wildcard meaning of that character
• if seqname /\w \ . \d/
• -This would match any sequence ID that has some
  text characters, a dot, followed by a single
  digit M65783.2

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Grabbing parts of a string

• Regular expressions can do more than just ask
  if questions
• They can be used to extract parts of a line of
  text into variables Check this out
• /gt(\w)\s(. )/
• Complete gibberish, right?
• It means
• -look for the gt sign at the beginning of a FASTA
  formatted sequence file
• -dump the first word (\w) into variable 1 (the
  sequence ID)
• -after a space, dump the rest of the line (.),
  until you reach the end of line , into variable
  2 (the description)

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You can also do Substitution

• To replace one string with another, use the
  tricky s/// function
• It works like this s/expression/replacement/
• text s/C-/A/
• (If only life were as easy as Perl)

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Thats all the Perl Im going to try to teach
yall.

• You know enough now to learn more from perl
  documentation, a book, or a website
• gt man perlintro
• gt man perlrequick
• Linconl Steins Genome Informatics class at CSHL
• http//stein.cshl.org/genome_informatics/index.ht
  ml
• Other cool websites
• http//www.troubleshooters.com/codecorn/littperl/p
  erlreg.htm