sed_wrapper.sh $silent $input $output '$url_paste' value.find('\'')==-1 normal silent **What it does** This tool runs the unix **sed** command on the selected data file. .. class:: infomark **TIP:** This tool uses the **extended regular** expression syntax (same as running 'sed -r'). **Further reading** - Short sed tutorial (http://www.linuxhowtos.org/System/sed_tutorial.htm) - Long sed tutorial (http://www.grymoire.com/Unix/Sed.html) - sed faq with good examples (http://sed.sourceforge.net/sedfaq.html) - sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf) - Collection of useful sed one-liners (http://student.northpark.edu/pemente/sed/sed1line.txt) ----- **Sed commands** The most useful sed command is **s** (substitute). **Examples** - **s/hsa//** will remove the first instance of 'hsa' in every line. - **s/hsa//g** will remove all instances (beacuse of the **g**) of 'hsa' in every line. - **s/A{4,}/--&--/g** will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&** marker is a place holder for 'whatever matched the regular expression'. - **s/hsa-mir-([^ ]+)/short name: \\1 full name: &/** will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'. The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) . **sed's Regular Expression Syntax** The select 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. **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.