Gene Count from GFF3 file

Question

[Mbillah]

We used the MAKER pipeline to predict genes from our recently assembled genome.

After filtering we tried to annotate our predicted genes with InterProScan.

Now we want to count how many genes the InterProScan has annotated?

[lieven.sterck]

cut -f1 <iprscan output file> | sort -u | wc -l

simply count the number of predicted gene IDs in the interpro output file

[Juke34]

You could give a try to this script gff3_sp_functional_statistics.pl from the GAAS repository. You will end up with something like that. This one is a bit verbose (Functions come from interproscan analysis) compare to what you can get in your case.

 ________________________________________________________________________________________
|          |  Nb term linked to mRNA |    Nb mRNA with term    |    Nb gene with term    |
|________________________________________________________________________________________|
|  PANTHER |            67           |            36           |            28           |
|________________________________________________________________________________________|
|   Pfam   |            37           |            36           |            29           |
|________________________________________________________________________________________|
|   PRINTS |            1            |            1            |            1            |
|________________________________________________________________________________________|
| SUPERFAMI|            21           |            19           |            14           |
|________________________________________________________________________________________|
|   Coils  |            16           |            16           |            12           |
|________________________________________________________________________________________|
|   Gene3D |            17           |            16           |            12           |
|________________________________________________________________________________________|
|    CDD   |            7            |            7            |            4            |
|________________________________________________________________________________________|
| ProSitePa|            3            |            3            |            3            |
|________________________________________________________________________________________|
|   SMART  |            12           |            10           |            6            |
|________________________________________________________________________________________|
| InterPro |            84           |            39           |            32           |
|________________________________________________________________________________________|
| MobiDBLit|            39           |            39           |            29           |
|________________________________________________________________________________________|
| Ontology_|            58           |            27           |            21           |
|________________________________________________________________________________________|
|  TIGRFAM |            1            |            1            |            1            |
|________________________________________________________________________________________|
| ProSitePr|            20           |            14           |            10           |
|________________________________________________________________________________________|
| Reactome |            54           |            2            |            2            |
|________________________________________________________________________________________|

nb mRNA without Functional annotation (CDD,Coils,Gene3D,InterPro,MobiDBLite,Ontology_term,PANTHER,PRINTS,Pfam,ProSitePatterns,ProSiteProfiles,Reactome,SMART,SUPERFAMILY,TIGRFAM)=  0
nb mRNA with Functional annotation (CDD,Coils,Gene3D,InterPro,MobiDBLite,Ontology_term,PANTHER,PRINTS,Pfam,ProSitePatterns,ProSiteProfiles,Reactome,SMART,SUPERFAMILY,TIGRFAM) = 110  
nb gene without Functional annotation (CDD,Coils,Gene3D,InterPro,MobiDBLite,Ontology_term,PANTHER,PRINTS,Pfam,ProSitePatterns,ProSiteProfiles,Reactome,SMART,SUPERFAMILY,TIGRFAM) = 0  
nb gene with Functional annotation (CDD,Coils,Gene3D,InterPro,MobiDBLite,Ontology_term,PANTHER,PRINTS,Pfam,ProSitePatterns,ProSiteProfiles,Reactome,SMART,SUPERFAMILY,TIGRFAM) = 72  

We found 17 gene with <Name> attribute. 
We found 28 mRNA with <Name> attribute. They probably have the same names as their parent genes. 
We have 110 mRNA with <product> attribute.