Extracting assembly accession number and protein ID using e-utilities

Question

[geizetomazetto]

Hi Folks,

I am trying to use my list of protein IDs (e.,g VUX63899.1,QDO61010.1, QDO50771.1) to retrieve the assembly accession number.

Using the follow commands ..

epost -input teste.txt -db protein | elink -target nuccore -db protein | elink -target assembly |esummary | xtract -pattern AssemblyAccession -element AssemblyAccession > assemblyAccession.txt

However, I need two columns with assembly accession with its corresponding protein IF. I could not figure out yet what the command I need to add.

Any tips?

Thanks in advance.

[Morgan S.]

Hi, did you ever solve this?

[geizetomazetto]

Hi Morgan,

Yes, I did. Thanks. Best,

Answer 1

[GenoMax]

Using EntrezDirect:

$ more id
VUX63899.1
QDO61010.1
QDO50771.1

Since epost method does not keep track of the original ID, use the following:

$ for i in `cat id`; do printf ${i}"\t"; esearch -db protein -query ${i} | elink -target nuccore | elink -target assembly |  esummary | xtract -pattern AssemblyAccession -element AssemblyAccession; done
VUX63899.1      GCF_902167535.1
QDO61010.1      GCF_007113405.2
QDO50771.1      GCF_007113445.1