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  • How to obtain gene ids from an .xml file

    Hi all,

    I have an .xml file from a blast search and I would like to extract the gene identifiers. Is it possible?

    Thanks in advance,

  • #2
    If this is a standard XML file from NCBI blast then this should work.

    Code:
    $ grep "Hit_accession" your_file.xml | sed 's/<Hit_accession>//' | sed 's/<\/Hit_accession>//'
    If you need the gi numbers then replace "Hit_accession" with "Hit_id".
    Last edited by GenoMax; 04-08-2014, 07:36 AM.

    Comment


    • #3
      It works perfectly! Thank you very much GenoMax!

      Comment

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