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Genes With List of Go terms

Hello,

I have a column of GO terms, and each GO term has a list of associated Genes in the second column.

term id         term name                            genes in term
GO:0005737  cytoplasm                      Gene 1 | Gene 2 | Gene 3 
GO:0032502  developmental process          Gene 1 | Gene 2 | Gene 3
GO:0048856 anatomical structure development    Gene 1 | Gene 2 | Gene 3

I want to change the format so I have a column of Genes, and followed by a list of associated GO terms.

gene                GO terms
Gene 1            cytoplasm | developmental process |  anatomical structure development
Gene 2            cytoplasm | developmental process |  anatomical structure development
Gene 3            cytoplasm | developmental process |  anatomical structure development

What is the best way to do this?

go-terms go
• 1,387 views • link
updated by Ram Ram • written by cthangav • cthangav

By 'what is the best way', I assume you have tried to do it or you might have some general ideas. If you share those people would be able to help you by considering your approach.

• 0 views • link
written by Hamid Ghaedi Hamid Ghaedi

1 answer

assuming tab delimited input:

awk -F '\t' '/^term/ {next} {N=split($3,a,/[ ]*[\|][ ]*/);for(i=1;i<=N;i++) printf("%s\t%s\n",a[i],$2);}'  input.txt |\
sort -t $'\t' -k1,1 |\
datamash groupby 1 unique 2

Gene 1  anatomical structure development,cytoplasm,developmental process
Gene 2  anatomical structure development,cytoplasm,developmental process
Gene 3  anatomical structure development,cytoplasm,developmental process
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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