text find_and_replace.pl #if $searchwhere.choice == "column": -c $searchwhere.column #end if -o $output $caseinsensitive $wholewords $skip_first_line $is_regex '$url_paste' '$file_data' '$input' value.find('\'')==-1 value.find('\'')==-1 entire line specific column **What it does** This tool finds & replaces text in an input dataset. .. class:: infomark The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box). .. class:: infomark When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 ) .. class:: infomark This tool uses Perl regular expression syntax. ----- **Examples of *regular-expression* Find Patterns** - **HELLO** The word 'HELLO' (case sensitive). - **AG.T** The letters A,G followed by any single character, followed by the letter T. - **A{4,}** Four or more consecutive A's. - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. - **hsa-mir-([^ ]+)** The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern. **Examples of Replace Patterns** - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&** (ampersand) represents the matched find pattern. - **\\1** The text which matched the first parenthesis in the Find Pattern. ----- **Example 1** **Find Pattern:** HELLO **Replace Pattern:** WORLD **Regular Expression:** no **Replace what:** entire line Every time the word HELLO is found, it will be replaced with the word WORLD. ----- **Example 2** **Find Pattern:** ^chr **Replace Pattern:** (empty) **Regular Expression:** yes **Replace what:** column 11 If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet" ----- **Perl's Regular Expression Syntax** The Find & Replace tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text. - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. - **^** matches the beginning of a string(but not an internal line). - **(** .. **)** groups a particular pattern. - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. - **{n}** The preceding item is matched exactly n times. - **{n,}** The preceding item ismatched n or more times. - **{n,m}** The preceding item is matched at least n times but not more than m times. - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. - **.** Matches any single character except a newline. - ***** The preceding item will be matched zero or more times. - **?** The preceding item is optional and matched at most once. - **+** The preceding item will be matched one or more times. - **^** has two meaning: - matches the beginning of a line or string. - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. - **$** matches the end of a line or string. - **\\|** Separates alternate possibilities. - **\\d** matches a single digit - **\\w** matches a single letter or digit or an underscore. - **\\s** matches a single white-space (space or tabs).