parse xml to tabular format

[simpson]

Hi, I've done blastx with -m 7 option. The output file is .xml.
But i'd like to do a data analysis to know the percentage of my unigene set has a blast hit. So i want to cover the .xml to another format.
Does anyone know any script that can do this?
Thanks,
Vivi

[GenoMax]

See this thread on Biostar: http://www.biostars.org/p/7290/

Stand-alone parser: https://github.com/pjotrp/blastxmlparser

[simpson]

See this thread on Biostar: http://www.biostars.org/p/7290/

Stand-alone parser: https://github.com/pjotrp/blastxmlparser

I had already seen that website. But that seems not work. Do you have more specific script and command that i can use directly?

[maubp]

If you specifically want to regenerate the BLAST+ tabular output, try this (standalone) Python script of mine:
https://bitbucket.org/peterjc/galaxy...ar.py?at=tools *DEAD LINK*
https://github.com/peterjc/galaxy_bl..._to_tabular.py *NEW LINK*

This is available with a Galaxy wrapper on the Galaxy Tool Shed as part of the BLAST+ suite:

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

[simpson]

If you specifically want to regenerate the BLAST+ tabular output, try this (standalone) Python script of mine:

https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_plus/blastxml_to_tabular.py?at=tools

This is available with a Galaxy wrapper on the Galaxy Tool Shed as part of the BLAST+ suite:
http://toolshed.g2.bx.psu.edu/view/d...cbi_blast_plus

Thanks. another question: how could i execute the python script? Can you give me the command please?

[maubp]

Thanks. another question: how could i execute the python script? Can you give me the command please?

Download the 'raw' python script and save it in your folder as blastxml_to_tabular.py then:

$ python blastxml_to_tabular.py
Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)

For example, if you want the standard 12 column tab separated variables,

$ python blastxml_to_tabular.py example.xml example.tsv std

If you want more details, it does an extended 24 column output mode too:

$ python blastxml_to_tabular.py example.xml example.tsv ext

The command line interface was deliberately minimal as this was intended primarily for use via the Galaxy interface.

[simpson]

Download the 'raw' python script and save it in your folder as blastxml_to_tabular.py then:

$ python blastxml_to_tabular.py
Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)

For example, if you want the standard 12 column tab separated variables,

$ python blastxml_to_tabular.py example.xml example.tsv std

If you want more details, it does an extended 24 column output mode too:

$ python blastxml_to_tabular.py example.xml example.tsv ext

The command line interface was deliberately minimal as this was intended primarily for use via the Galaxy interface.

Traceback (most recent call last):
File "xml.py", line 70, in <module>
import xml.etree.cElementTree as ElementTree
File "/scratch/hpc/tianwenl/blastall/xml.py", line 70, in <module>
import xml.etree.cElementTree as ElementTree
ImportError: No module named etree.cElementTree
[tianwenl@submit1 blastall]$ module load python
[tianwenl@submit1 blastall]$ python xml.py jatropha.unigene20.nr.xml jatropha.tabular.tsv ext
Traceback (most recent call last):
File "xml.py", line 70, in <module>
import xml.etree.cElementTree as ElementTree
File "/scratch/hpc/tianwenl/blastall/xml.py", line 70, in <module>
import xml.etree.cElementTree as ElementTree
ImportError: No module named etree.cElementTree
[tianwenl@submit1 blastall]$ python xml.py jatropha.unigene20.nr.xml jatropha.tabular.tsv std
Traceback (most recent call last):
File "xml.py", line 70, in <module>
import xml.etree.cElementTree as ElementTree
File "/scratch/hpc/tianwenl/blastall/xml.py", line 70, in <module>
import xml.etree.cElementTree as ElementTree
ImportError: No module named etree.cElementTree

[maubp]

What version of python do you have?

[simpson]

What version of python do you have?

it is biopython 1.59

[maubp]

This script doesn't use Biopython - I meant which version of Python do you have? e.g. python 2.5?

[simpson]

This script doesn't use Biopython - I meant which version of Python do you have? e.g. python 2.5?

sorry - -

Python 2.6.6 (r266:84292, Oct 12 2012, 14:23:48)

[maubp]

Strange. The cElementTree library would normally be included with Python, however I've updated the script to fall back on the pure Python ElementTree library instead. Could you try that please (same link - that points at the latest version)? Thanks.

[simpson]

it's working now!!!
Thank you very much!!

Strange. The cElementTree library would normally be included with Python, however I've updated the script to fall back on the pure Python ElementTree library instead. Could you try that please (same link - that points at the latest version)? Thanks.

[amitbik]

Hi.. maubp

I want to convert blast xml output to tabular form. I followed your link but it is not opening.
Can you send the again?

Thank you......

[maubp]

Hi.. maubp

I want to convert blast xml output to tabular form. I followed your link but it is not opening.
Can you send the again?

Thank you......

Sorry - the old BitBucket link is dead now, that code moved to GitHub:

https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/blastxml_to_tabular.py