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how to parse XML blast output

Hello everyone, (I am not native in English)

I want to parse XML local blast result (transcripts against NCBI nr) to see the name of the transcripts that have shown any hits (if the name of the transcripts and the name of the protein could be retrieve, it is better).

it seems that Biophython NCBIXML is designed for this work.

Would you please help me for a simple script to run NCBIXML on my output.xml ?

Thank you in advance

NOTE:

1- I have checked some related posts, but could not figure it out.

2- If there is any other software or package for this "parsing", mention it, please.

blast biopython ncbixml
• 3,671 views • link
written by Farbod Farbod

Hi Alex Reynolds and thank you,

would you please suggest any script for recieving the below results from the blastx XML ?

name of transcripts                       annotation
    Trinity-1                              proteinX
    Trinity-3                              proteinY
• 0 views • link
written by Farbod Farbod

Now I am using BlastParse.pl, a perl script, And I want some more flexible software.

• 0 views • link
written by Farbod Farbod

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