add excercise

docs/pages/bash_manip/bash_manip-7-sed.md

@@ -49,7 +49,7 @@ sed 'FLAG/<pattern>/<string>/FLAG'
     |----------|----------| ----| ----| ----| ----| ----| ----|
     q | Quit after a line (`/<pattern>/q` or `<integer>q`) | | x | x | | | |
     d | Delete lines (`/<pattern>/d` or `<integer>d`) | | x | x | | | |
-    p | Print matched lines (`-n '/<pattern>/p'`) | | | x | | | |
+    p | Print matched lines (`-n '/<pattern>/p'`) | Only with `-n` option | | x | | | |
     a | Append text after a line (`/<pattern>/a Add new text after`) | On macOS (BSD sed) the command requires a backslash (`\`) and a newline. | | | x | | |
     i | Insert text before a line (`/<pattern>/i Add new text before`) | On macOS (BSD sed) the command requires a backslash (`\`) and a newline | | | x | | |
     c | Change entire line (`/<pattern>/c This is a new line`) | | | | x | | |
@@ -63,7 +63,7 @@ sed 'FLAG/<pattern>/<string>/FLAG'
 
 ## Line selection 
 
-**Syntax**
+### Syntax
 
 ```bash
 sed -n 'line p' file
@@ -79,10 +79,13 @@ sed -n 'line p' file
 | `sed '8,$ p' file` | Print lines from line 8 to the end of the file |
 | `sed -n '1~8 p' file` | Print from line 1, every 8 lines |
 
+### Exercice
+
+
 
 ## Line deletion 
 
-**Syntax**
+### Syntax
 
 ```bash
 sed 'line d' file
@@ -97,9 +100,13 @@ sed 'line d' file
 | `sed '8,$ d' file` | Delete lines from line 8 to the end of the file |
 | `sed '1~8d' file` | Delete from line 1, every 8 lines |
 
+### Exercice
+
+
+
 ## Use of Regular Expression 
 
-**Syntax**
+### Syntax
 
 ```bash
 sed 'RegEx' file
@@ -110,9 +117,13 @@ sed 'RegEx' file
 | `sed '/^#/d' file` | Delete lines starting by # |
 | `sed -n '/\tmRNA\t/p' file` | Print lines matchin mRNA surrounded by tabulation |
 
+### Exercice
+
+
+
 ## Subsitution
 
-**Syntax**
+### Syntax
 
 ```bash
 sed 's/pattern/replacement/' file
@@ -126,20 +137,37 @@ sed 's/pattern/replacement/' file
 | `s/pattern/replacement/i` | Substitute the first occurrence of pattern with replacement, ignoring case |
 | `s/pattern/replacement/gi` | Substitute all occurrences of pattern with replacement, ignoring case |
 
-## Extract value
+### Exercice
+
+
+
+## Capturing
 
 It is possible to extract part of a line. Let's take the example of the extraction of a value from an attribute (`tag=value`) with tag `Name` of the 9th column of a GFF/GTF file.
 
-**Syntax**
+### Syntax
 
 ```bash
-sed 's/.*Name=\([^;]*\);.*/\1/p' file
+sed -n 's/.*START\([^END]*\)END.*/\1/p' file.txt
 ```
 
 * `-n` Suppresses default output (only prints matches).
 * `s/.../.../p` Substitutes text and prints only the matched part.
-* `.*Name=` Matches everything before Name=.
-* `\([^;]*\)` Captures everything after Name= until the first ;.
-* `.*` Matches everything after ; (but doesn’t capture it).
-* `\1` Outputs only the captured group (the Name value).
-* `/p` Prints the result.
+* `.*` Matches anything before the START marker.
+* `START` The fixed pattern before the part we want.
+* `\(` Start of capture group (tells sed to remember this part).
+* `[^END]*` Captures everything until it reaches the END marker.
+* `\)` End of capture group.
\ No newline at end of file
+* `END` The fixed text after the part we want.
+* `.*` Matches everything after the END marker.
+* `\1` Prints the first captured group (here only 1 has been captured).
+* `p` Explicitly prints the result (only used with -n).
+
+### Exercice
+
+!!! question "List all names that are associated to PIERRE (e.g. OLIVIER that is used to do PIERRE-OLIVER)"
+
+??? example "Click to show the solution"  
+    ```bash
+    sed -n 's/.*;PIERRE-\([^;]*\);.*/\1/p' nat2021.csv | sort -u
+    ```