BLAST convert xml to tabular format

[SDPA_Pet]

Hi, can anyone help me find a tool which can convert xml blast output format to tabular. It's better to support blast+.

Thank you.

Ben

[lindenb]

See https://www.biostars.org/p/7290/ Question: Tools Parsing Ncbi Blast -M 7 Xml Output Format?

[SDPA_Pet]

Any other tools with GUI version? I am not familiar with perl

[maubp]

Here's my Python script https://github.com/peterjc/galaxy_bl..._to_tabular.py with Galaxy wrapper https://github.com/peterjc/galaxy_bl...to_tabular.xml - does that count as a GUI?

[SDPA_Pet]

Here's my Python script https://github.com/peterjc/galaxy_bl..._to_tabular.py with Galaxy wrapper https://github.com/peterjc/galaxy_bl...to_tabular.xml - does that count as a GUI?

Hi thanks. I download your scripts and save it as blastxml_to_tabular.py. How should I use it.

should I type python blastxml_to_tabular.py -i nitrogen.xml -o nitrogen.txt.

I am sorry about this kind of newbie questions. I am a biological student. I don't have any background of computer sciences.

I attached the blastxml_to_tabular.py. Please have a quick look and see the format is correct or not.

[maubp]

It looks like you got the Galaxy XML file by mistake. This https://github.com/peterjc/galaxy_bl..._to_tabular.py is the pretty Human Readable page for the Python script, this https://raw.githubusercontent.com/pe..._to_tabular.py link will download the script itself ready to run.

Are you using Linux, Mac OS X, or Windows? If Windows you will also need to install Python and running it is a little more complicated. Linux and the Mac should already have a suitable version of Python installed.

[SDPA_Pet]

I tried on windows but it says some errors.

Can you give me an example of using this script, if I want to convert 12 column txt file.

[maubp]

What errors? If you copy/paste the message here it would be far easier to guide you - but I guess part of the problem is you are using -i which is not expected.

Assuming you installed Python 2.7, you would run something like this - the default is the standard 12 column output:

C:\Python27\python blastxml_to_tabular.py -o nitrogen.txt nitrogen.xml

[SDPA_Pet]

Hi, I want to convert xml to txt?

should it be python blastxml_to_tabular.py nitrogen.xml -o nitrogen.txt

do I need to type an "-i" in front of "nitrogen.xml"

The error is invalid data format

[maubp]

In this case, either is fine:

python blastxml_to_tabular.py -o nitrogen.txt nitrogen.xml

python blastxml_to_tabular.py nitrogen.xml -o nitrogen.txt

Note that in general many command line tools are fussy about the exact order.

What does your file "nitrogen.xml" look like? Can you share it via http://gist.github.com or perhaps show the first ten lines here inside [ code ] and [ /code ] tags?

(The code tags are available via the forum's advanced editor view using the "#" icon.)

[SDPA_Pet]

BLAST-like file generated by MEGAN


Query=HZKDEPY02FP29T

>ref|YP_003433234.1| glutamine synthetase [Hydrogenobacter thermophilus TK-6]
ref|YP_005512249.1| glutamine synthetase, type I [Hydrogenobacter thermophilus TK-6]
ref|WP_012964213.1| glutamine synthetase [Hydrogenobacter thermophilus]
dbj|BAI70033.1| glutamine synthetase [Hydrogenobacter thermophilus TK-6]
gb|ADO45956.1| glutamine synthetase, type I [Hydrogenobacter thermophilus TK-6]
Length = 469

Score = 80.9 bits (198), Expect = 1e-13
Identities = 35/39 (89%), Positives = 39/39 (100%)
Frame = -2

Query: 161 PLTRERYGRDTRYVAQKAEQYLRQTGIGDTAYFGPEAEF 45
P+TRERYGRDTRY+AQKAEQYL+QTGIGDTAY+GPEAEF
Sbjct: 98 PITRERYGRDTRYIAQKAEQYLKQTGIGDTAYYGPEAEF 136

>ref|YP_003474070.1| glutamine synthetase [Thermocrinis albus DSM 14484]
ref|WP_012992349.1| glutamine synthetase [Thermocrinis albus]
gb|ADC89943.1| glutamine synthetase, type I [Thermocrinis albus DSM 14484]
Length = 469

Score = 80.9 bits (198), Expect = 1e-13
Identities = 35/39 (89%), Positives = 39/39 (100%)
Frame = -2

Query: 161 PLTRERYGRDTRYVAQKAEQYLRQTGIGDTAYFGPEAEF 45
P+TRERYGRDTRY+AQKAEQYL+QTGIGDTAY+GPEAEF
Sbjct: 98 PITRERYGRDTRYIAQKAEQYLKQTGIGDTAYYGPEAEF 136

>ref|YP_007499517.1| glutamine synthetase, type I [Hydrogenobaculum sp. HO]
ref|YP_007646578.1| glutamine synthetase, type I [Hydrogenobaculum sp. SN]
ref|WP_015418780.1| glutamine synthetase, type I [Hydrogenobaculum sp. HO]
gb|AEF18544.1| glutamine synthetase, type I [Hydrogenobaculum sp. 3684]
gb|AEG45832.1| glutamine synthetase, type I [Hydrogenobaculum sp. SHO]
gb|AGG14474.1| glutamine synthetase, type I [Hydrogenobaculum sp. HO]
gb|AGH92778.1| glutamine synthetase, type I [Hydrogenobaculum sp. SN]
Length = 469

Score = 80.1 bits (196), Expect = 2e-13
Identities = 35/39 (89%), Positives = 38/39 (97%)
Frame = -2

Query: 161 PLTRERYGRDTRYVAQKAEQYLRQTGIGDTAYFGPEAEF 45
P+TRERYGRDTRY+AQKAEQYL+QTGIGD AYFGPEAEF
Sbjct: 97 PITRERYGRDTRYIAQKAEQYLKQTGIGDVAYFGPEAEF 135

[maubp]

BLAST XML output looks like this, and is designed for a computer to read:

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastp</BlastOutput_program>
  <BlastOutput_version>BLASTP 2.2.24+</BlastOutput_version>
  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>nr</BlastOutput_db>
  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
  <BlastOutput_query-def>Sample</BlastOutput_query-def>
  <BlastOutput_query-len>516</BlastOutput_query-len>
...

Your results look like plain text BLAST output

[SDPA_Pet]

The one I posted earlier is extract from megan.

I have the original file but it didn't work either. Here it is

BLASTX 2.2.20 [Feb-08-2009]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= HZKDEPY02G6265
(375 letters)

Database: /nfs/scratch/sdpapet/db/mpidatabase/NCBI05252013nr
25,805,290 sequences; 8,915,431,356 total letters



Score E
Sequences producing significant alignments: (bits) Value

ref|YP_003474070.1| glutamine synthetase [Thermocrinis albus DSM... 220 1e-55
ref|YP_003433234.1| glutamine synthetase [Hydrogenobacter thermo... 219 3e-55
ref|YP_002120801.1| glutamine synthetase, type I [Hydrogenobacul... 204 9e-51
ref|YP_007499517.1| glutamine synthetase, type I [Hydrogenobacul... 202 6e-50
ref|NP_213074.1| glutamine synthetase [Aquifex aeolicus VF5] >gi... 199 5e-49
ref|WP_008286412.1| glutamine synthetase [Hydrogenivirga sp. 128... 196 3e-48
ref|YP_002731353.1| glutamine synthetase, type I [Persephonella ... 187 1e-45
ref|YP_002728028.1| glutamine synthetase [Sulfurihydrogenibium a... 187 1e-45
ref|YP_001931244.1| glutamine synthetase, type I [Sulfurihydroge... 183 2e-44
ref|WP_007545780.1| glutamine synthetase, type I [Sulfurihydroge... 183 3e-44

>ref|YP_003474070.1| glutamine synthetase [Thermocrinis albus DSM 14484]
ref|WP_012992349.1| glutamine synthetase [Thermocrinis albus]
gb|ADC89943.1| glutamine synthetase, type I [Thermocrinis albus DSM 14484]
Length = 469

Score = 220 bits (561), Expect = 1e-55
Identities = 104/110 (94%), Positives = 107/110 (97%)
Frame = +2

Query: 26 KHGPALTAFTNPTINSYHRLVPGFEAPVRLAYSARNRSAAIRIPTYSQSPKAKRIEIRFP 205
KHGPALTAFTNPT+NSYHRLVPGFEAPVRLAYSARNRSAAIRIPTYSQSPKAKRIEIRFP
Sbjct: 303 KHGPALTAFTNPTVNSYHRLVPGFEAPVRLAYSARNRSAAIRIPTYSQSPKAKRIEIRFP 362

Query: 206 DPTCNPYLAFSAILMAAIDGVENKIHPGEPFDKDIYSLPPEELKDIPNCP 355
DPTCNPYLAFSAILMAAIDG+EN+IHPGEP DKDIYSLPPEELKDIP P
Sbjct: 363 DPTCNPYLAFSAILMAAIDGIENRIHPGEPLDKDIYSLPPEELKDIPQLP 412

[maubp]

That file is also just plain text BLAST output.

[SDPA_Pet]

Oh, when I did the blast I use -m 7 and it says it is xml format. Is there any software to convert this to tabular format? I used the old BLAST not BLAST+