Export ensembl efetch in comma-delimited format

Question

[marongiu.luigi]

Hello

I am using ensembl to extract taxonomic data of some sequences. I tried to save the output into a bash variable with three columns and then extract the three columns afterwards:

hit=$(efetch -db taxonomy -id $tax -format native -mode xml | xtract -pattern TaxaSet -element ScientificName | head -1 | cut -f 1,3,7)
fam=$(echo $hit | awk '{print $(NF)})
kin=$(echo $hit | awk '{print $(NF-1)})

but fam and kin are empty. This thing works by running xtract each time:

hit=$(efetch -db taxonomy -id $tax -format native -mode xml | xtract -pattern TaxaSet -element ScientificName | head -1 | cut -f 1)
fam=$(efetch -db taxonomy -id $tax -format native -mode xml | xtract -pattern TaxaSet -element ScientificName | head -1 | cut -f 3)
kin=$(efetch -db taxonomy -id $tax -format native -mode xml | xtract -pattern TaxaSet -element ScientificName | head -1 | cut -f 7)

Is there a way to export efetch/xtract in comma-delimited so cutting the results is easier?

Thank you

Answer 1

[GenoMax]

I am using ensembl to extract taxonomic data of some sequences

Small nitpick but you are using EntrezDirect, not Ensembl.

Following works for me. Using your example code with 9606 taxID. I think you are missing a single quote in your awk commands.

$ hit=$(efetch -db taxonomy -id 9606 -format native -mode xml | xtract -pattern TaxaSet -element ScientificName | head -1 | cut -f 1,3,7)
$ echo $hit
Homo sapiens Eukaryota Bilateria

$ fam=$(echo $hit | awk '{print $NF}')
$ echo $fam
Bilateria

$ kin=$(echo $hit | awk '{print $(NF-1)}')
$ echo $kin
Eukaryota