This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Using Batch Entrez to extract .gb files with specific coordinates

Hello everyone, I have a list of ID's and coordinates (Start position-End position) for each ID that I need to download as a .gb file from the NCBI database. Is there a possible way to Fetch them all using Batch Entrez? Every ID has it's own specific coordinates. eg.:

ID: CP005986.1 Start: 1600000 End: 1620000

What kind of a file do I have to make, so that Batch Entrez recognizes each argument? Thanks a lot!

ncbi batch-entrez genbank
• 1,934 views • link
written by vykintas.jauniskis • vykintas.jauniskis

1 answer

Batch entrez may not be the right tool in this case since it seems to retrieve the entire record. You can use NCBI eUtils to do this e.g. efetch -db nuccore -format gb -id CP005986 -chr_start 1600000 -chr_stop 1620000 will get you the segment you are looking for.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this