Using Batch Entrez to extract .gb files with specific coordinates

Question

[vykintas.jauniskis]

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!

Answer 1

[GenoMax]

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.