Mapping gene names to GO ids

Question

[Ric]

Hello, I downloaded goa_uniprot_all.gaf 4.4.GB) as shown below:

!gaf-version: 2.1
!
!This file contains all GO annotations and gene product information for proteins in the UniProt KnowledgeBase (UniProtKB),
!IntAct protein complexes, and RNAcentral identifiers.
!
!Generated: 2017-09-25 14:48 
!GO-version: http://purl.obolibrary.org/obo/go/releases/2017-09-23/extensions/go-plus.owl
!
UniProtKB       OEL25522.1  moeA5           GO:0003824      GO_REF:0000002  IEA     InterPro:IPR015421|InterPro:IPR015422   F       MoeA5   A0A000_9ACTN|moeA5      protein taxon:35758     20170923        InterPro                
UniProtKB       XP_021321391.1  moeA5           GO:0003870      GO_REF:0000002  IEA     InterPro:IPR010961      F       MoeA5   A0A000_9ACTN|moeA5      protein taxon:35758     20170923        InterPro                    
UniProtKB       ABQ44355.1  moeA5           GO:0009058      GO_REF:0000002  IEA     InterPro:IPR004839      P       MoeA5   A0A000_9ACTN|moeA5      protein taxon:35758     20170923        InterPro                   
UniProtKB       XP_004953070.1  moeA5           GO:0030170      GO_REF:0000002  IEA     InterPro:IPR004839|InterPro:IPR010961   F       MoeA5   A0A000_9ACTN|moeA5      protein taxon:35758     20170923        InterPro                
UniProtKB       XP_004953070.1  moeA5           GO:0033014      GO_REF:0000002  IEA     InterPro:IPR010961      P       MoeA5   A0A000_9ACTN|moeA5      protein taxon:35758     20170923        InterPro

I have also a file which contain my mapped trinity contings to swissprot as shown below:

target_id       ens_gene
lcl|ScwjSwM_1   OEL25522.1
lcl|ScwjSwM_2   XP_021321391.1
lcl|ScwjSwM_3   ABQ44355.1
lcl|ScwjSwM_4   XP_004953070.1

To get the mapping the 2nd columns from both files could be used to create a file which has the following 2 columns (contig names, GO ids) e.g. lcl|ScwjSwM_4,GO:0030170|GO:0033014. What would be the best way to do it?

Thank you in advance.

Answer 1

[Pierre Lindenbaum]

To get the mapping the 2nd columns from both files could be used to create a file which has the following 2 columns (contig names, GO ids) e.g. lcl|ScwjSwM_4,GO:0030170|GO:0033014. What would be the best way to do it?

use join

join -t $'\t' -1 2 -2 2 \
  <(sort -t $'\t' -k2,2  goa_uniprot_all.gaf ) \
  <(sort -t $'\t' -k2,2 swissprot.tsv )

followed by a cut command to extract the column...

Answer 2

[e.rempel]

Hi,

if you would like to use R for your analysis, you could use command merge.