Update AWK_module.md

Finding_and_summarizing_colossal_files/lessons/AWK_module.md

@@ -338,6 +338,29 @@ It works! We can see that "moose,bison" is the most commonly observed group of a
 </details>
 ****
 
+### Bioinformatic Application
+
+Counting can be a great way to summarize different annotation files (gff, gff3, gtf etc). This is especially true when working with new files that have been generated by other people. Here is the gff we showed above but slightly edited
+
+```
+chr3	entrez	five_prime_UTR	50252100	50252137	.	+	.	ID=UTR5:ENST00000266027.9;Parent=ENST00000266027.9;gene_id=ENSG00000114353.17;transcript_id=ENST00000266027.9;gene_type=protein_coding;gene_name=GNAI2;transcript_type=protein_coding;transcript_name=GNAI2-201;exon_number=2;exon_id=ENSE00003567505.1;level=3;protein_id=ENSP00000266027.6;transcript_support_level=2;hgnc_id=HGNC:4385;tag=basic,CCDS;ccdsid=CCDS63644.1;havana_gene=OTTHUMG00000156940.2
+chr3	ENSEMBL	three_prime_UTR	50257691	50257714	.	+	.	ID=UTR3:ENST00000266027.9;Parent=ENST00000266027.9;gene_id=ENSG00000114353.17;transcript_id=ENST00000266027.9;gene_type=protein_coding;gene_name=GNAI2;transcript_type=protein_coding;transcript_name=GNAI2-201;exon_number=8;exon_id=ENSE00003524043.1;level=3;protein_id=ENSP00000266027.6;transcript_support_level=2;hgnc_id=HGNC:4385;tag=basic,CCDS;ccdsid=CCDS63644.1;havana_gene=OTTHUMG00000156940.2
+chr3	entrez	three_prime_UTR	50258368	50259339	.	+	.	ID=UTR3:ENST00000266027.9;Parent=ENST00000266027.9;gene_id=ENSG00000114353.17;transcript_id=ENST00000266027.9;gene_type=protein_coding;gene_name=GNAI2;transcript_type=protein_coding;transcript_name=GNAI2-201;exon_number=9;exon_id=ENSE00001349779.3;level=3;protein_id=ENSP00000266027.6;transcript_support_level=2;hgnc_id=HGNC:4385;tag=basic,CCDS;ccdsid=CCDS63644.1;havana_gene=OTTHUMG00000156940.2
+chr3	ENSEMBL	gene	50227436	50227490	.	+	.	ID=ENSG00000275334.1;gene_id=ENSG00000275334.1;gene_type=miRNA;gene_name=MIR5787;level=3;hgnc_id=HGNC:49930
+chr3	entrez	gene	52560570	52560707	.	+	.	ID=ENSG00000221518.1;gene_id=ENSG00000221518.1;gene_type=snRNA;gene_name=RNU6ATAC16P;level=3;hgnc_id=HGNC:46915
+chr3	ENSEMBL	transcript	52560570	52560707	.	+	.	ID=ENST00000408591.1;Parent=ENSG00000221518.1;gene_id=ENSG00000221518.1;transcript_id=ENST00000408591.1;gene_type=snRNA;gene_name=RNU6ATAC16P;transcript_type=snRNA;transcript_name=RNU6ATAC16P-201;level=3;transcript_support_level=NA;hgnc_id=HGNC:46915;tag=basic,Ensembl_canonical
+```
+
+The second column tells us where the annotation comes from and the third column tells us what kind of feature it is. Both of these columns can be useful to summarize when you are starting to work with a new gtf file.
+
+```bash
+awk ' { counter[$2] += 1 } END { for (source in counter){ print source, counter[source] } }' my_gtf.gtf
+```
+
+
+```bash
+awk ' { counter[$3] += 1 } END { for (feature in counter){ print feature, counter[feature] } }' my_gtf.gtf
+```
 
 ## MFC
 
@@ -352,7 +375,7 @@ samtools view -S -b ${sam}.sam > ${sam}.bam
 done
 ```
 
-This actually combines a number of basic and intermediate shell topics such as [positional parameters](positional_params.md), [for loops](loops_and_scripts.md), and `awk`!
+This actually combines a number of basic and intermediate shell topics such as [positional parameters]([positional_params.md](https://hbctraining.github.io/Training-modules/Accelerate_with_automation/lessons/positional_params.html)), [for loops](https://hbctraining.github.io/Training-modules/Accelerate_with_automation/lessons/loops_and_scripts.html), and `awk`!
 
 * We start with a for loop that counts from 1 to 10
 
@@ -391,6 +414,8 @@ Why do you think that this is MFC?
 
 # Additional cool `awk` commands
 
+For these commands we will return to ecosystems.txt
+
 ### BEGIN
 
 The `BEGIN` command will execute an `awk` expression once at the beginning of a command. This can be particularly useful it you want to give an output a header that doesn't previously have one.
@@ -403,7 +428,7 @@ In this case we have told `awk` that we want to have "new_header" printed before
 
 ### END
 
-Related to the `BEGIN` command, the `END` command that tells `awk` to do a command once at the end of the file. It is ***very*** useful when summing up columns (below), but we will first demonstrate how it works by adding a new record:
+We already had some experience with `END` above. Related to the `BEGIN` command, the `END` command that tells `awk` to do a command once at the end of the file. We will first demonstrate how it works by adding a new record:
 
 ```
 awk '{print $1} END {print "new_record"}' ecosystems.txt