Regular expressions

1
Regular expressions

• NB Must appear within forward slashes (/)
• Some operators
• marks the start of a string /glu/
  begins with glu
• marks the end of a string /ase/
  ends with ase
• . dot is any single character
• characters in square brackets are regarded as
  a set, any of which can be matched
• 0-9 specifies a range of 1 to 9
• the preceding group may be repeated zero or
  more times
• the preceding group may be repeated one or more
  times
• ? The preceding character/group occurs one or
  zero times

2
Some examples

• /glu/ will find terms
  beginning with glu
• /ase/ will find terms
  ending with ase
• /c.t/ will find the
  words cat, cot, cut.
• /c.t/ will find terms
  beginning with c and
• then any number of
  characters and ending with t
• /smiyth/ will find the words
  smith or smyth
• /rho1-9/ will find the word rho
  followed by a number from 1-9
• /mue?ller/ will find muller or
  mueller
• NB. The symbol has two meanings
• -within forward slashes / it means the
  preceding group may be
• repeated zero or more times
• - outside forward slashes it means any
  character

3
Numerical ranges

• In a numerical index it is possible to search
  numerical ranges
• - sequence lengths, mol. weights, dates.
• the is used for specifying ranges and !
  for excluding values
• 400500 all seq. with length between 400 and
  500
• 400 all seq. with lengths greater
  than 400
• 500 all seq. with lengths less than
  500
• 400!500 all seq. with lengths bet. 400 and
  500 excluding 500
• Can combine ranges using logical operators
• 300!400 !500600 or 300600 !
  400500
• Dates in SRS have 2 formats
• YYYYMMDD 20021205
• DD-MMM-YYYY 05-Dec-2002

4
Links programacion

• http//nsaunders.wordpress.com/2006/12/01/automate
  d-srs-retrieval-using-perl-and-lwp/
• http//www.srs-user.org.uk/dokuwiki/doku.php
• http//www.ebi.ac.uk/srs/wiki/doku.php?idguides
  srsurlapi
• http//www.srs-user.org.uk/dokuwiki/doku.php?idpr
  ojectsbasicsrsapiperl