This vignette summarizes examples from:
Haddock, S.H.D., and C.W. Dunn. 2011. Practical Computing For Biologists. Sinauer Associates, Sunderland, MA.
\w for a single character\w+ for one or more characters(\w+) to capture the first word\1 to replace with the first capturefind: (\w)(\w+) (\w+)
Myrmica lobrifons
replace: \1. \3
M. lobifrons
replace: \1. \3 \1_\3
M. lobifrons M_lobifrons
replace: \1\2 \3 \1_\3
Myrmica lobifrons M_lobifrons\In a text editor, duplicate two lines of text and progressively do the search on 1 line to get it correct. Then build up the replace terms. Use \ to escape special characters
Original text Myrmica punctiventris (Wheeler)
Search with matches \w+ \w+ \( \w+ \)
Text with captures (\w+) (\w+) \( (\w+) \)
Remove extra space (\w+) (\w+) \((\w+)\)
Replacement text \1_\2_\3
Result Myrmica_punctiventris_Wheeler\w A word character, including letters, numbers, & underscore
\t A tab character (can also be used in replacements)
\s A white space character, including tabs, spaces, and the end of the line
\n End-of-line marker (can also be used in replacements)
\r Carriage return
\d A digit from 0 to 9
. Any letter, number or symbol except end-of-line charactersUse these in combination for more general searches
Original text +38 30.5'N
Mark captures (+38) (30.5)'N
Regular expressions with wild cards (.\d+) (\d+.\d+).\w+
Replacement text \1\t\2\t
Result 38 30.5[]Use a pair of brackets to create a custom character set
[AGCT]+ finds one or more A G C or T
[0-9\.] finds any digit or decimal point
[A-Za-z] finds lower or upper case letters
[A-Z\-] finds upper case letters and dashUse character sets to find ending marks and fuse lines
Original text 21 17`24.69"N
157 51`41.50"W
Mark captures (\"[NS]}\r
Replacement text \1\t
Result 21 17`24.69"N 157 51`41.50"WSearch [^A-Z\r]
Replace x
Result Anything except a capital letter and end of line is an `x`
Search ([^\t]+)\t
Result Captures a column of tab-delimited text\ and endings $Use the ^ and the $ to mark the boundary at the beginning and the end of a line, respectively.
Original text Myrmica lobifrons
Mark captures ^(\w)\w+
Replacement text \1\.
Result M. lobifronsUse * as a quantifier for 0 or more, in contrast to + for one or more. Thus, the all-inclusive wildcard .* should grab any leftovers up to the end of the line following specific text.
Original text Myrmica lobifrons
Mark captures (Myr).*
Replacement text \1
Result Myr?Whereas + captures 1 or more elements, and * captures 0 or more elements, adding ? after the modifier captures the minimum number of elements. Use this to capture text before a repeat. For example, to capture everything but a terminal string of A, use
Original text CCTCAAGTAAAAA
Search (\w+?)A*$
Replacement text \1
Result CCTCAAGT{}Follow an expression with curly brackets to indicate the exact number of matches. For example A{5} searches for a string of 5 As, whereas C{2,6} searches for the a string of Cs that is at least 2 but no more than 6 in length. And a search for G{6,} looks for a minimum of 6, but more if it can find them. Here are two other examples:
Original text CTAAGAGAAAAAAAA
Search A{8,}
Replacement text -nothing-
Result CTAAGAG
Original text 34.23457444
Search (\d*\.}(\d{3})d+
Replacement text \1\2
Result 34.234OPERATION FIND REPLACE
Split elements like nano_128.dat (\w+)_(\d+)\.(\w+) \1\t\2\t\3
Merge or rearrange columns of values (\w+)\t(\w+) \2 \1
Join multiple lines into one \n [or maybe \r] ,
Split a single line into multiple lines , \n
Convert a list of names to move the first (.*) (\w+)$ \2 \1
name and initials to the end, separated by
a comma (won't work with "Jr.," etc.)XBeginning to last occurrence ^.*X(.*)
Beginning to first occurrence ^[^X\r]*(X)
Beginning to first occurrence (alternate) ^.*(X)
After the first occurrence to the end (X).*?$
Up to the last occurrence ^.*(X)
(CAUTION: Finding no match for x deletes the line)