add flags

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

-# Extracting from files
+# SED
 
+## setup
 
-```bash
-# or curl -O instead of wget
-wget https://ftp.ensembl.org/pub/release-113/gff3/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.113.gff3.gz
-gunzip Saccharomyces_cerevisiae.R64-1-1.113.gff3.gz
-mv Saccharomyces_cerevisiae.R64-1-1.113.gff3 yeast.gff
-```
-
-You should now have a file called `yeast.gff` in your working directory.
-
-```
-##gff-version 3
-###
-I	sgd	gene	335	649	.	+	.	ID=gene:YAL069W;biotype=protein_coding;description=Dubious open reading frame%3B unlikely to encode a functional protein%2C based on available experimental and comparative sequence data [Source:SGD%3BAcc:S000002143];gene_id=YAL069W;logic_name=sgd
-I	sgd	mRNA	335	649	.	+	.	ID=transcript:YAL069W_mRNA;Parent=gene:YAL069W;biotype=protein_coding;tag=Ensembl_canonical;transcript_id=YAL069W_mRNA
-I	sgd	exon	335	649	.	+	.	Parent=transcript:YAL069W_mRNA;Name=YAL069W_mRNA-E1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=YAL069W_mRNA-E1;rank=1
-I	sgd	CDS	335	649	.	+	0	ID=CDS:YAL069W;Parent=transcript:YAL069W_mRNA;protein_id=YAL069W
-###
-```
-
-The GFF/GTF format describe genomics features, such as genes, exons, CDS in a standardized format.
-Every line starting with `#` is a comment. 
-Each line is a feature and contains 9 fields (tabulation separated).
+??? quote "First click and follow the instructions below only if you start the course at this stage! Otherwise skip this step!"
+    {%
+    include-markdown "pages/bash_manip/bash_manip-0-setup.md"
+    %}
 
 
 ## Concept
@@ -44,7 +27,39 @@ sed [Option(s)] 'Command(s)' [File(s)]
     | -r | Use extended regular expressions in the script
     | -s | Treat files as separate rather than as a single continuous long stream
 
-At our level the options most useful would be `-n` and `-i`
+At our level the options the most useful would be `-n`, `-i` and `-e`
+
+Skipping the option part, `sed` commands can be shaped in different way :
+<pattern>
+```bash
+# case1 by line number
+sed '<integer>FLAG'
+# case2 by line matching
+sed '/<pattern>/FLAG'
+# case2.2 by line matching
+sed '/<pattern>/FLAG <string>'
+# case3 by match
+sed 'FLAG/<pattern>/<string>/'
+# case3.2 by match
+sed 'FLAG/<pattern>/<string>/FLAG'
+```
+
+??? Note "Available FLAGs"
+    | Command | Description | Comment | Case1 `sed '<integer>FLAG'` | Case2 `sed '/<pattern>/FLAG'`| Case2.2 `sed '/<pattern>/FLAG <string>'` | Case3 `sed 'FLAG/<pattern>/<string>/'` | Case3.2 `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 | | | |
+    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 | | |
+    y | character transliteration (`y/<characters>/<characters>/`) | | | | | x | |
+    s | Substitute first match on each line (`s/<pattern>/<string>/`) | | | | | x | |
+    s + g | Global - Substitute all occurrences on each line (`s/<pattern>/<string>/g`) | | | | | x |  x |
+    s + i | Case-insensitive - Substitute all occurrences on each line (`s/<pattern>/<string>/i`) | | | | | x | x |
+    s + p | Print modified lines (`s/<pattern>/<string>/p`) | | | | | x | x |
+    s + g + i + p | A combination of s + flags i,p,g is possilbe (`s/<pattern>/<string>/pig`) | | | | | x | x |
+
 
 ## Line selection 
 
@@ -58,6 +73,8 @@ sed -n 'line p' file
 |----------|----------|
 | `sed -n '8p' file` | Print line 8 |
 | `sed -n '8p; 16p' file` | Print lines 8 and 16 |
+| `sed -n '8p; 16p' file` | Print lines 8 and 16 |
+| `sed -n -e '8p' -e '16p' file` | Print lines 8 and 16 |
 | `sed -n '8,16 p' file` | Print lines from 8 to 16 |
 | `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 |
@@ -75,6 +92,7 @@ sed 'line d' file
 |----------|----------|
 | `sed '8d' file` | Delete line 8 |
 | `sed '8d; 16d' file` | Delete lines 8 and 16 |
+| `sed -e '8d' -e '16d' file` | Delete lines 8 and 16 |
 | `sed '8,16 d' file` | Delete lines from 8 to 16 |
 | `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 |