Question: Using entrez-direct inside a for loop in bash
0
gravatar for Lille My
15 months ago by
Lille My30
Lille My30 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 • 502 views
ADD COMMENTlink modified 15 months ago by genomax85k • written 15 months ago by Lille My30

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 REPLYlink written 15 months ago by Joe17k
0
gravatar for genomax
15 months ago by
genomax85k
United States
genomax85k 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 COMMENTlink modified 15 months ago • written 15 months ago by genomax85k
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