Hi, Thanks for the code, It works fine, but In my file, In the second column, I have 11 IDs for a gene 'Fer'. So, I should get the pathway names of them separated by commas in a column. To be more specific, All pathway names of that gene should be in one column. Similarly, for all other genes.
How to get Kegg pathway names from kegg pathway IDs
Hello,
I 'm trying to find the pathway names corresponding to pathway IDs of mus musculus in R. My input file is in the form below. Kegg_ID
- 4520
- 04145, 04514, 04650, 04670, 04810, 05140, 05144, 05146, 05150, 05323, 05416
- 4622
- 00561, 00564, 01100, 04070
I found some working codes in other posts, but those input files contain only one ID per column. Please help me.
Thanks in advance.
2 answers
GeneSCF 'prepare_database' module downloads KEGG-ID, description and genes associated with the terms as simple table format (plain text file).
./prepare_database -db=KEGG -org=mmu
The above command downloads complete KEGG db as simple text file in following location, 'geneSCF-tool/class/lib/db/mmu/'.
$ sed 's/, /\n/g' test.txt | awk '{printf("%05d\n", $1)}' | parallel wget -qO- http://togows.org/entry/kegg-pathway/mmu{}/pathways >> pathways.txt
output:
$ cat pathways.txt
mmu04520 Adherens junction
mmu04145 Phagosome
mmu04514 Cell adhesion molecules (CAMs)
mmu04650 Natural killer cell mediated cytotoxicity
mmu04670 Leukocyte transendothelial migration
mmu04810 Regulation of actin cytoskeleton
mmu05140 Leishmaniasis
mmu05144 Malaria
mmu05146 Amoebiasis
mmu05150 Staphylococcus aureus infection
mmu05323 Rheumatoid arthritis
mmu05416 Viral myocarditis
mmu04622 RIG-I-like receptor signaling pathway
mmu00561 Glycerolipid metabolism
mmu00564 Glycerophospholipid metabolism
mmu01100 Metabolic pathways
mmu04070 Phosphatidylinositol signaling system
input:
$ cat test.txt
4520
04145, 04514, 04650, 04670, 04810, 05140, 05144, 05146, 05150, 05323, 05416
4622
00561, 00564, 01100, 04070
This is the example data.
GENE_NAME KEGG_ID
- Klf6 NULL
- Fer 04145, 04514, 04650, 04670, 04810, 05140, 05144, 05146, 05150, 05323, 05416 3.Itgb2l 04622
Expected Output : GENE_NAME KEGG_ID PathwayName
- Klf6 NULL 2.Fer 04520 Adherens junction
- Fer 04145,04514...... Phagosome,Cell adhesion molecules (CAMs),Natural killer cell mediated cytotoxicity,Leukocyte transendothelial migration,Regulation of actin cytoskeleton,Leishmaniasis,Malaria,Amoebiasis,Staphylococcus aureus infection,Rheumatoid arthritis,Viral myocarditis
code:
$awk -F"\t" '{split($2,a,","); for(i in a)print $1"\t"a[i]}' test.txt | awk -v OFS="\t" '{$1=$1}1'| awk '{ printf "%s\tmmu%05d\n", $1,$2 }' > test_out.txt
$a=$(cut -f2 test_out.txt | tr '\n' ',' ) && wget -qO- http://togows.org/entry/kegg-pathway/$a/pathways | sed 's/ /\t/' > pathways.txt
$join -t $'\t' -1 2 -2 1 <(sort -k2 test_out.txt) <(sort -k1 pathways.txt) | datamash -sg2 unique 1,3
Input (replace x1,x2,x3 and x4 with appropriate genes):
$ cat test.txt
x1 4520
x2 04145, 04514, 04650, 04670, 04810, 05140, 05144, 05146, 05150, 05323, 05416
x3 4622
x4 00561, 00564, 01100, 04070
output:
x1 mmu04520 Adherens junction
x2 mmu04145,mmu04514,mmu04650,mmu04670,mmu04810,mmu05140,mmu05144,mmu05146,mmu05150,mmu05323,mmu05416 Amoebiasis, Cell adhesion molecules (CAMs), Leishmaniasis, Leukocyte transendothelial migration, Malaria, Natural killer cell mediated cytotoxicity, Phagosome, Regulation of actin cytoskeleton, Rheumatoid arthritis, Staphylococcus aureus infection, Viral myocarditis
x3 mmu04622 RIG-I-like receptor signaling pathway
x4 mmu00561,mmu00564,mmu01100,mmu04070 Glycerolipid metabolism, Glycerophospholipid metabolism, Metabolic pathways, Phosphatidylinositol signaling system
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