This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

(Please note that the original software licenses still apply)

This image allows the usage of the Entrez Direct⁠ utilities, including:

• Navigation functions support exploration within the Entrez databases:

  • esearch performs a new Entrez search using terms in indexed fields.
  • elink looks up neighbors (within a database) or links (between databases).
  • efilter filters or restricts the results of a previous query.

• Records can be retrieved in specified formats or as document summaries:

  • efetch downloads records or reports in a designated format.

• Desired fields from XML results can be extracted without writing a program:

  • xtract converts EDirect XML output into a table of data values.

• Several additional functions are also provided:

  • einfo obtains information on indexed fields in an Entrez database.
  • epost uploads unique identifiers (UIDs) or sequence accession numbers.
  • nquire sends a URL request to a web page or CGI service.

Using the Entrez Direct image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/entrez-direct <entrez-direct-command> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <entrez-direct-command> to the name of the Entrez Direct command you want to use.
• <options> with the specific options of the Entrez Direct command. These options will include the input/output files if required, which should be referenced under /data/.

Examples

Example 1: retrieve FASTA sequences from accession numbers

To download the FASTA sequences from the accession numbers XM_016057909.1 and XM_030992799.1, the epost and efetch commands can be used. The steps are:

• Create a file named accessions.txt with these accessions.
• Run epost using the accessions file as input and write the result to epost.result.
• Run efetch using the epost.result as input and write result to sequences.fastap.

echo -e "XM_016057909.1\nXM_030992799.1" > accessions.txt
docker run --rm -v /your/data/dir:/data pegi3s/entrez-direct epost -db nuccore -format uid -input /data/accessions.txt > epost.result
docker run --rm -v /your/data/dir:/data pegi3s/entrez-direct bash -c "efetch -format fasta < /data/epost.result > /data/sequences.fasta"

Alternatively, the output of the epost command can be piped to the efetch command:

docker run --rm -v /your/data/dir:/data pegi3s/entrez-direct bash -c "echo -e \"XM_016057909.1\nXM_030992799.1\" | epost -db nuccore -format uid | efetch -format fasta > /data/sequences.fasta"

Example 2: retrieve taxonomy information for a given species

To retrieve the taxonomy information for a for a given species, the esearch and efetch commands can be used. For instance, the following commands downloads the taxonomy of Homo sapiens into a taxonomy.xml file:

docker run --rm -v /your/data/dir:/data pegi3s/entrez-direct bash -c "esearch -db taxonomy -query "Homo+sapiens" | efetch -db taxonomy -format xml > /data/taxonomy.xml"