<p>The most human-readable blast output formats are 0-4, e.g. <code>-outfmt 0</code> - which if I am not mistaken is the format used by web blast. However, these formats are a pain to automatically parse.</p>
<p>As <a href="https://bioinformatics.stackexchange.com/a/13732/1642">Cowboy_Patrick</a> pointed out, XML is more of a machine-readable format. The tabular output format ( <code>-outfmt 6</code>) is very commonly used, because it is easily parsed by unix command-line tools, and its structure also allows a somewhat easy human reading and understanding.</p>

CC BY-SA 4.0
2020-07-07T11:41:44.423Z
Many thanks, how to set the output format as -outfmt 6 in a line of python code as
 result = NCBIWWW.qblast('blastn','nt',ADN.format('fasta') ) ?
serpipanton
CC BY-SA 4.0
2020-07-07T14:46:08.283Z
@serpipanton I am unfamiliar with BioPython, but a cursory look at the documentation suggests -outfmt 6 is unavailable for NCBIWWW.qblast. However, there is a module NCBIXML, which will allow you to easily parse the xml output.
h.mon
CC BY-SA 4.0
2020-07-05T21:01:06.107Z
2020-07-06T02:04:14.933Z
2020-07-06T02:04:14.933Z
h.mon
<p>Is this what you are looking for: <a href="https://codebeautify.org/xmlviewer" rel="nofollow noreferrer">https://codebeautify.org/xmlviewer</a> ? XML is a format designed to be readable firstly by machines, not humans.</p>
<p>With xslt you can convert XML to various more readable formats see this blog for something that fits your XML: <a href="http://plindenbaum.blogspot.com/2008/05/ncbi-blast-xslt-xhtml-svg.html?m=1" rel="nofollow noreferrer">http://plindenbaum.blogspot.com/2008/05/ncbi-blast-xslt-xhtml-svg.html?m=1</a></p>

CC BY-SA 4.0
2020-07-05T17:47:55.637Z
2020-07-05T17:47:55.637Z
Cowboy_Patrick
<p>I got a blast xml file after a DNA sequence search. The XML file is not very readable. What is the way to make it more understandable? This blast contains about twenty matches. <a href="https://www.grosfichiers.com/Hm7h8kqcjW5" rel="nofollow noreferrer">Here is the xml file</a></p>

CC BY-SA 4.0
2020-07-05T21:26:35.953Z
You can do this using the Bio Entrez parser in Biopython. Its quite easy to use, but its not clear whether your happy using Python.
M__
<blast>
how to have a blast xml file in a readable and understandable way
# how to have a blast xml file in a readable and understandable way

(Asked by: username_0 on 2020-07-05)

I got a blast xml file after a DNA sequence search. The XML file is not very readable. What is the way to make it more understandable? This blast contains about twenty matches. [Here is the xml file](https://www.grosfichiers.com/Hm7h8kqcjW5)

**Tags:** blast
> **Comments:**
> **username_1**: You can do this using the Bio Entrez parser in Biopython. Its quite easy to use, but its not clear whether your happy using Python.  

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## 2 answers

### Answer by username_2 on 2020-07-05. Score: 2

The most human-readable blast output formats are 0-4, e.g. `-outfmt 0` - which if I am not mistaken is the format used by web blast. However, these formats are a pain to automatically parse.

As [Cowboy\_Patrick](https://bioinformatics.stackexchange.com/a/13732/1642) pointed out, XML is more of a machine-readable format. The tabular output format ( `-outfmt 6`) is very commonly used, because it is easily parsed by unix command-line tools, and its structure also allows a somewhat easy human reading and understanding.

> **Comments:**
> **username_0**: Many thanks, how to set the output format as -outfmt 6 in a line of python code as  result = NCBIWWW.qblast('blastn','nt',ADN.format('fasta') ) ?  
> **username_2**: @serpipanton I am unfamiliar with BioPython, but a cursory look at the documentation suggests -outfmt 6 is unavailable for NCBIWWW.qblast. However, there is a module NCBIXML, which will allow you to easily parse the xml output.  

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### Answer by username_3 on 2020-07-05. Score: 1

Is this what you are looking for: <https://codebeautify.org/xmlviewer> ? XML is a format designed to be readable firstly by machines, not humans.

With xslt you can convert XML to various more readable formats see this blog for something that fits your XML: <http://plindenbaum.blogspot.com/2008/05/ncbi-blast-xslt-xhtml-svg.html?m=1>


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