improve and fix #1

docs/pages/bash_manip/bash_manip-5-grep2.md

@@ -10,6 +10,12 @@
 
 ## Searching patterns (grep)
 
+In order to use regular expression in grep you should use the `-E` option:  
+
+```bash
+grep -E pattern file
+```
+
 Back to our data file `nat2021.csv` containing first names given to children born in France since 1900.  
 Let's play with some RegEx...
 

docs/pages/bash_manip/bash_manip-6-awk.md

@@ -12,7 +12,6 @@
 
 `AWK` is a powerful programming language designed for text processing and typically used as a data extraction and reporting tool. Named after its creators (Aho, Weinberger, and Kernighan), `AWK` is particularly well-suited for processing **columnar data** and performing complex text manipulations.
 
-
 ```bash
 awk 'BEGIN { Initial action(s) } /pattern/ { by line action(s) } END { final action(s) }' file
 ```
@@ -41,11 +40,85 @@ RS | The record separator, which determines how awk separates input records. Def
 FNR | The record number in the current input file (resets for each new file).
 ARGV | An array containing the command-line arguments passed to awk.
 
+## Built-in Functions
+
+Awk provides built-in functions for string manipulation and numeric operations, making it a powerful tool for text processing and calculations.
+
+### Numeric Manipulation
+
+awk includes several numeric functions for performing mathematical operations.
+
+| Function | Description
+|----------|----------|
+sin(x) | Returns the sine of x (x in radians)
+cos(x) | Returns the cosine of x (x in radians)
+atan2(y, x) | Returns the arctangent of y/x
+log(x) | Returns the natural logarithm of x
+exp(x) | Returns the exponential of x
+sqrt(x) | Returns the square root of x
+int(x) | Returns the integer part of x
+rand() | Returns a random number between 0 and 1
+srand([x]) | Sets the seed for rand() and returns the previous seed
+
+### String Manipulation
+
+Awk provides several string functions to manipulate text. 
+
+| Function | Description
+|----------|----------|
+length([string]) | Returns the length of the string (or the length of $0 if no string is given)
+substr(string, start, [length]) | Returns the substring of string starting at start position with optional length
+index(string, search) | Returns the position of search in string, or 0 if not found
+match(string, regex) | Returns the position of the match of regex in string, or 0 if no match
+split(string, array, [separator]) | Splits string into array elements using separator (default is FS)
+tolower(string) | Returns a copy of string with all characters converted to lowercase
+toupper(string) | Returns a copy of string with all characters converted to uppercase
+sprintf(format, expressions) | Returns a formatted string using format and expressions
+
 ## Programmation in awk
 
-awk is a full-fledged programming language that supports control structures such as if-else and loops, making it powerful for text processing. Here’s a brief overview:
+awk is a full-fledged programming language that use two type of data structure (variable and array) and supports control structures such as if-else and loops, making it powerful for text processing. Here’s a brief overview:
+
+### Data Structure
 
-### if/else statement
+**variable**
+
+```bash
+var = string # Assigns a value to a variable
+var = $1+$2 # calculation
+```
+
+**array**
+
+AWK arrays use keys instead of just numerical indices (like dictionaries in Python). They are dynamic i.e. no need to declare the size; you can add elements anytime.
+
+```bash
+# fill an array
+array["fruit1"] = apple;
+array["fruit2"] = banana;
+array["fruit3"] = cherry;
+
+# delete an entry
+delete array[fruit2]
+
+# print results
+for(key in array){         # Traversing through key array here.
+     print key,array[key]  # Printing index and value of current item
+}
+
+```
+
+It is possible to split a String into an Array:
+
+```bash
+awk 'BEGIN {
+    str = "apple,banana,cherry";
+    split(str, myArray, ",");
+    print myArray[1];  # Output: apple
+}'
+```
+
+### If/else Statement
 
 ```bash
 awk '{ if (condition) { action1 } else { action2 } }' file.txt
@@ -76,13 +149,23 @@ You can combine conditions using logical operators:
 
 **Pattern Matching with Regular Expressions**
 
-You can use regular expressions with the ~ (matches) or !~ (does not match) operators.
+You can use the following approach:  
+
+```bash
+awk '/pattern/ { by line action(s) }' file
+```
+
+Or you can use regular expressions with the ~ (matches) or !~ (does not match) operators.
 
 | Operator | Description
 |----------|----------|
 ~ | Matches a regex pattern
 !~ | Does NOT match a regex pattern
 
+```bash
+awk '{ if ($2 ~ /pattern/) }' file
+```
+
 ### loop
 
 You can also use for loops and while loops in awk.

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

@@ -63,7 +63,7 @@ sed 'FLAG/<pattern>/<string>/FLAG'
 
 ## Line selection 
 
-### Syntax
+**Syntax**
 
 ```bash
 sed -n 'line p' file
@@ -78,7 +78,7 @@ 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 | `~` not supported by BSD sed (MacOS)
 
-### Exercice
+**Exercice**
 
 !!! question "Print the header and line 686 529 until the end."
 
@@ -90,7 +90,7 @@ sed -n 'line p' file
 
 ## Line deletion 
 
-### Syntax
+**Syntax**
 
 ```bash
 sed 'line d' file
@@ -105,7 +105,7 @@ 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 | `~` not supported by BSD sed (MacOS)
 
-### Exercice
+**Exercice**
 
 !!! question "Delete everything from line 10 to 686 529."
 
@@ -116,7 +116,7 @@ sed 'line d' file
 
 ## Use of Regular Expression 
 
-### Syntax
+**Syntax**
 
 ```bash
 sed 'RegEx' file
@@ -144,7 +144,7 @@ sed 'RegEx' file
     {n,m} | Matches between n and m occurrences (Extended Regex) | sed -E 's/a{2,4}/c/g'
     \ | Escapes special characters | sed 's/\./X/g'
 
-### Exercice
+**Exercice**
 
 !!! question "Select all line that match PIERRE in the 2000s."
 
@@ -155,7 +155,7 @@ sed 'RegEx' file
 
 ## Subsitution
 
-### Syntax
+**Syntax**
 
 ```bash
 sed 's/pattern/replacement/' file
@@ -169,7 +169,7 @@ 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 |
 
-### Exercice
+**Exercice**
 
 !!! question "Replace all numbers from last colum by XX"
 
@@ -190,7 +190,7 @@ sed 's/pattern/replacement/' file
 
 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 -n 's/.*START\([^END]*\)END.*/\1/p' file.txt
@@ -208,7 +208,7 @@ sed -n 's/.*START\([^END]*\)END.*/\1/p' file.txt
 * `\1` Prints the first captured group (here only 1 has been captured).
 * `p` Explicitly prints the result (only used with -n).
 
-### Exercice
+**Exercice**
 
 !!! question "List all names that are associated to PIERRE (e.g. OLIVIER that is used to do PIERRE-OLIVER)"