gff file

Question

[devhimd]

I have a GFF file of the UniProt I want to extract the lipidation, modified residue and its modifications, and the residue number on how to do that?

I want only the lipidation, modified residue, and its modifications, residue number in a CSV file

Is there any programming code or awk script to do that?

[manaswwm]

I think it would be better if you post a sample of the gff file and what you want to extract from it

[devhimd]

##gff-version 3
##sequence-region P01112 1 189
P01112  UniProtKB   Chain   1   186 .   .   .   ID=PRO_0000042996;Note=GTPase HRas  
P01112  UniProtKB   Initiator methionine    1   1   .   .   .   Note=Removed%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.12 
P01112  UniProtKB   Chain   2   186 .   .   .   ID=PRO_0000326476;Note=GTPase HRas%2C N-terminally processed    
P01112  UniProtKB   Propeptide  187 189 .   .   .   ID=PRO_0000042997;Note=Removed in mature form   
P01112  UniProtKB   Nucleotide binding  13  18  .   .   .   Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16698776;Dbxref=PMID:16698776    
P01112  UniProtKB   Nucleotide binding  29  35  .   .   .   Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16698776;Dbxref=PMID:16698776    
P01112  UniProtKB   Nucleotide binding  59  60  .   .   .   Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16698776;Dbxref=PMID:16698776    
P01112  UniProtKB   Nucleotide binding  116 119 .   .   .   Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16698776;Dbxref=PMID:16698776    
P01112  UniProtKB   Nucleotide binding  145 147 .   .   .   Note=GTP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16698776;Dbxref=PMID:16698776    
P01112  UniProtKB   Region  166 185 .   .   .   Note=Hypervariable region   
P01112  UniProtKB   Motif   32  40  .   .   .   Note=Effector region    
P01112  UniProtKB   Modified residue    1   1   .   .   .   Note=N-acetylmethionine%3B in GTPase HRas%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.12    
P01112  UniProtKB   Modified residue    2   2   .   .   .   Note=N-acetylthreonine%3B in GTPase HRas%2C N-terminally processed;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.12    
P01112  UniProtKB   Modified residue    118 118 .   .   .   Note=S-nitrosocysteine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9020151;Dbxref=PMID:9020151    
P01112  UniProtKB   Modified residue    186 186 .   .   .   Note=Cysteine methyl ester;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8626715;Dbxref=PMID:8626715    
P01112  UniProtKB   Lipidation  181 181 .   .   .   Note=S-palmitoyl cysteine;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15705808,ECO:0000269|PubMed:16000296,ECO:0000269|PubMed:2661017,ECO:0000269|PubMed:8626715;Dbxref=PMID:15705808,PMID:16000296,PMID:2661017,PMID:8626715 
P01112  UniProtKB   Lipidation  184 184 .   .   .   Note=S-(15-deoxy-Delta12%2C14-prostaglandin J2-9-yl)cysteine%3B alternate;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12684535;Dbxref=PMID:12684535   
P01112  UniProtKB   Lipidation  184 184 .   .   .   Note=S-palmitoyl cysteine%3B alternate;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15705808,ECO:0000269|PubMed:16000296,ECO:0000269|PubMed:2661017,ECO:0000269|PubMed:8626715;Dbxref=PMID:15705808,PMID:16000296,PMID:2661017,PMID:8626715    
P01112  UniProtKB   Lipidation  186 186 .   .   .   Note=S-farnesyl cysteine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8626715;Dbxref=PMID:8626715  
P01112  UniProtKB   Glycosylation   35  35  .   .   .   Note=(Microbial infection) O-linked (Glc) threonine%3B by P.sordellii toxin TcsL;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:19744486,ECO:0000269|PubMed:8626575,ECO:0000269|PubMed:8626586,ECO:0000269|PubMed:9632667;Dbxref=PMID:19744486,PMID:8626575,PMID:8626586,PMID:9632667    
P01112  UniProtKB   Cross-link  170 170 .   .   .   Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin);Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:30442762;Dbxref=PMID:30442762   
P01112  UniProtKB   Alternative sequence    152 189 .   .   .   ID=VSP_041597;Note=In isoform 2. VEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS->SRSGSSSSSGTLWDPPGPM;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14500341,ECO:0000303|PubMed:15489334;Dbxref=PMID:14500341,PMID:15489334  
P01112  UniProtKB   Natural variant 12  12  .   .   .   ID=VAR_026106;Note=In CSTLO. G->A;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16170316,ECO:0000269|PubMed:16329078,ECO:0000269|PubMed:16443854;Dbxref=dbSNP:rs104894230,PMID:16170316,PMID:16329078,PMID:16443854 

[devhimd]

This is the GFF file I want to extract only lipidation, nitrocysteine, and cysteine thioester from this file. I want to make a CSV file where it consists of the modification in one column and the residue numbers of the respective modification in another column. I don't want the other information like the evidence and the ECO etc...,.

So how should I proceed to write a program, awk script, or Perl script?

[manaswwm]

I suppose here you are referring to this gff file : https://www.uniprot.org/uniprot/P01112.gff

I am not a regular user of awk or Perl, but I am using R regularly so I can suggest a simple R script:

library(ape) #if ape is not installed then you can do so using  - install.packages("ape")

This is how you read gff:

uniprot_gff = read.gff("uniprot.gff", GFF3 = TRUE)

This is how you can subset the "table" of the gff file for column "type" which contains "lipidation", "nitrocysteine" and "cysteine" entries and also have its respective residue number:

  uniprot_gff_subset = uniprot_gff[uniprot_gff$type %in% c("Lipidation","Nitrocysteine","Cysteine"),][,c("type","start","end")]

[devhimd]

can you write using python?

[manaswwm]

I have been out of touch with python, but I am sure you can use similar logic (possibly even package) with python