how to parse XML blast output
0
0
Entering edit mode
5.1 years ago
Farbod ★ 3.3k

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 • 2.7k views
ADD COMMENT
0
Entering edit mode

There are many libraries in Python, but BeautifulSoup is an excellent and easy-to-use library for scraping HTML and XML: https://www.crummy.com/software/BeautifulSoup/

ADD REPLY
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1710 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6