Hi guys,
I got a metagenome sample and identified several species/families... in there. Now I'm thinking of automatically gathering pathways (just the names though) for each of those species. Preferably this should be done in R. Any Ideas of a Database / API where to download Pathway-Names given the species name?
Thanks,
Phil
to clarify, basically what I need is typing 'Gardnerella Vaginalis' into some KEGG (or any other) API and I retrieve the list of pathways, here just a snapshot
gvg00010 Glycolysis / Gluconeogenesis - Gardnerella vaginalis ATCC 14019
gvg00030 Pentose phosphate pathway - Gardnerella vaginalis ATCC 14019
gvg00040 Pentose and glucuronate interconversions - Gardnerella vaginalis ATCC 14019
gvg00051 Fructose and mannose metabolism - Gardnerella vaginalis ATCC 14019
gvg00052 Galactose metabolism - Gardnerella vaginalis ATCC 14019
gvg00061 Fatty acid biosynthesis - Gardnerella vaginalis ATCC 14019
gvg00071 Fatty acid degradation - Gardnerella vaginalis ATCC 14019
gvg00072 Synthesis and degradation of ketone bodies - Gardnerella vaginalis ATCC 14019
gvg00121 Secondary bile acid biosynthesis - Gardnerella vaginalis ATCC 14019
3 answers
•
written
by
umer.zeeshan.ijaz
This definitely looks like a great solution, will try it. Thanks!
Well you can always download the annotated GBK file from NCBI for different species. Put them all in a folder, use cat *.gbk > test.gbk and then keeping your fingers crossed that you have annotated enzymes, you can follow the one-liners then onwards.
Read this post of mine.
•
written
by
umer.zeeshan.ijaz
I guess this will be my work around if anything else fails. What I am thinking about at the moment is using the KEGGREST R API from Bioconductor. The only problem I got at the moment is that I'm not too sure about how to get the first list of pathways available at all. Because if I got those, I can just 'grep' for the T.genome numbers, download those and do what ever I want to them... This, might decrease traffic and therefore time...
I will keep you posted anyways what worked out best! If you have any other Idea let me know! But thanks for your help!!!!!!
Okay I spent last 20 mins thinking over this, and here is the solution ( I have to go somewhere now, I did it in a hurry so excuse a long one-liner, but I think I have done it right):
Step 1: Go to the website, and see which organisms/species are you interested in, and then get their T numbers (which is genome ID), and store them in IDs.txt
$ cat IDs.txt
T01329
T02919
T01060
T02994
Step 2: Now use the following to extract the pathways for your species/organism:
$ for i in $(cat IDs.txt); do echo $(curl -s http://rest.kegg.jp/link/pathway/genome:$i | grep -Po '(?<=path:).*') | awk '{gsub("[a-zA-Z]+","",$0);}1'| xargs -n 1 | xargs -I {} curl -s http://rest.kegg.jp/find/pathway/{} | awk -v k=$i '{print k"\t"$0}' ; done
T01329 path:map00010 Glycolysis / Gluconeogenesis
T01329 path:map00020 Citrate cycle (TCA cycle)
T01329 path:map00030 Pentose phosphate pathway
T01329 path:map00040 Pentose and glucuronate interconversions
T01329 path:map00051 Fructose and mannose metabolism
T01329 path:map00052 Galactose metabolism
T01329 path:map00053 Ascorbate and aldarate metabolism
T01329 path:map00061 Fatty acid biosynthesis
T01329 path:map00062 Fatty acid elongation
T01329 path:map00071 Fatty acid degradation
T01329 path:map00072 Synthesis and degradation of ketone bodies
T01329 path:map00100 Steroid biosynthesis
T01329 path:map00120 Primary bile acid biosynthesis
T01329 path:map00130 Ubiquinone and other terpenoid-quinone biosynthesis
T01329 path:map00140 Steroid hormone biosynthesis
T01329 path:map00190 Oxidative phosphorylation
T01329 path:map00230 Purine metabolism
T01329 path:map00232 Caffeine metabolism
T01329 path:map00240 Pyrimidine metabolism
T01329 path:map00250 Alanine, aspartate and glutamate metabolism
T01329 path:map00260 Glycine, serine and threonine metabolism
T01329 path:map00270 Cysteine and methionine metabolism
T01329 path:map00280 Valine, leucine and isoleucine degradation
T01329 path:map00290 Valine, leucine and isoleucine biosynthesis
T01329 path:map00300 Lysine biosynthesis
T01329 path:map00310 Lysine degradation
hey,
apologize distrubing you again but why I am not able to redirect the output into a file instead having it on the terminal? Is there any special way needed to do that?
I was trying it with:
...| awk -v k=$i '{print k"\t"$0 > "./foo.txt"}' ; done
or
...| awk -v k=$i '{print k"\t"$0}' ; done > ./foo.txt
but somehow this just creates the file but leaves it empty... (both times)
edit:
solved it. THANK YOU SO MUCH!!
The NCBI biosystems database contains a resource mapping the BSID to the taxon iD:
ftp://ftp.ncbi.nih.gov/pub/biosystems/CURRENT/biosystems_taxonomy.gz
•
written
by
Pierre Lindenbaum
Using the KEGG REST, wrote the following PERL script. Is this what you exactly wanted?
open FH,"pathwayIds.txt"; ##list of organisms in KEGG Org code
while(<FH>)
{
`wget http://rest.kegg.jp/list/pathway/$_`;
}
close(FH);
INPUT: pathwayIds.txt
gva
gvg
gvh
If you just have one organism, then type the following in terminal
wget http://rest.kegg.jp/list/pathway/gvg
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