Using entrez-direct inside a for loop in bash

Question: Using entrez-direct inside a for loop in bash

8 days ago by

Lille My • 30 wrote:

I'm trying to retrieve the genome from which a series of proteins are derived. there is more than one assembly for each protein, so I need to create a file where they are linked.

I use the following:

for id in `cat gi-list-file`; do
elink -target nuccore -db protein -id $id |
elink -target assembly |
esummary  |
 xtract -pattern AssemblyAccession -element AssemblyAccession
done

the first result I get is the assembly accession, but the second result is the following error message:

Retrying elink, step 2: callMLink: Error reading an UID blob, ,CNCHistory::ReadIdListBuf, result (false) error, blobid=empty

Any ideas on what the problem is?

bash ncbi • 81 views

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modified 8 days ago by genomax ♦ 64k • written 8 days ago by Lille My • 30

what happens if you run that accession directly outside of the loop?

Can you also show us some examples of accessions which work, and some that don't?

ADD REPLY • link written 8 days ago by jrj.healey ♦ 11k

8 days ago by

genomax ♦ 64k

United States

genomax ♦ 64k wrote:

Following works for me.

$ more names.txt
WP_043107373
WP_000617546.1
WP_000906486.1
WP_001096206.1
WP_001386830.1

Loop used for the lookups

$ for i in `cat names.txt`; do echo $i; elink -target nuccore -db protein -id $i |elink -target assembly|esummary |xtract -pattern AssemblyAccession -element AssemblyAccession > $i.txt; done

This should produce one file per input Accession number.

With a non-existent accession number an error will be generated and result in an empty file for that accession. Loop should continue for rest of the accession.

WP_031373
ERROR in link output: BLOB ID IS NOT IMPLEMENTED

Actual error message is larger, truncated for display.

ADD COMMENT • link modified 8 days ago • written 8 days ago by genomax ♦ 64k

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