comparison awk.xml @ 8:4c752559b236 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

7:01ca80da2266

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'
- **$5-$4>23**  will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23.
- **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
- **$7 ~ /A{4}U/**  will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
- If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).


**Action Examples**

- **{ print }** or **{ print $0 }**   will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'.
- **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
- **{ print $4, $5-$4 }** will print the fourth column and the difference between the fifth and fourth column. (If the fourth column was start-position in the input file, and the fifth column was end-position - the output file will contain the start-position, and the length).
- If no action part is specified (not even the curly brackets) - the default action is to print the entire line.


**AWK's Regular Expression Syntax**

8:4c752559b236

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'
- **$5-$4>23**  will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23.
- **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
- **$7 ~ /A{4}U/**  will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
- **BEGIN** will be executed once only, before the first input record is read. 
- If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).



**Action Examples**

- **{ print }** or **{ print $0 }**   will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'.
- **{ print $1, $4, $5 }** will print only the first, fourth and fifth fields of the input line.
- **{ print $4, $5-$4 }** will print the fourth column and the difference between the fifth and fourth column. (If the fourth column was start-position in the input file, and the fifth column was end-position - the output file will contain the start-position, and the length).
- **{ FS = "," }** can be used to change the field separator (delimeter) for parsing the input file.
- If no action part is specified (not even the curly brackets) - the default action is to print the entire line.


**AWK's Regular Expression Syntax**