Convert Blast output to tabular

Rsola · 08-27-2013, 06:52 AM

Hi,

Does anybody know how to convert Blast Output as below to a tabular (.csv) output or how to extract top hits? In the online tool that I use I can't select for tabular output.

Thanks!

Query= OsSNP0002
(142 letters)

Database: ../uniprot-oryza-sativa-indica.fasta
42,240 sequences; 15,872,719 total letters

Searching..................................................done

Score E
Sequences producing significant alignments: (bits) Value

tr|A2WJN5|A2WJN5_ORYSI Putative uncharacterized protein OS=Oryza... 55 2e-18
tr|B8AKP7|B8AKP7_ORYSI Putative uncharacterized protein OS=Oryza... 53 6e-17
tr|B8AEL6|B8AEL6_ORYSI Putative uncharacterized protein OS=Oryza... 28 1.5
tr|B8B114|B8B114_ORYSI Putative uncharacterized protein OS=Oryza... 28 2.0
tr|B8AQS5|B8AQS5_ORYSI Putative uncharacterized protein OS=Oryza... 27 2.6
tr|B8ADP7|B8ADP7_ORYSI Putative uncharacterized protein OS=Oryza... 27 4.4
tr|A2ZKU4|A2ZKU4_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5
tr|A2Y774|A2Y774_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5
tr|A2WXP8|A2WXP8_ORYSI Putative uncharacterized protein OS=Oryza... 25 9.7 [/SIZE][/SIZE]

lran2008 · 08-27-2013, 06:59 AM

You could choose the Blast output format by setting -outfmt. Try -outfmt 6 .

Rsola · 08-27-2013, 07:05 AM

Thank you for your reply, but like I indicated, I can't set the output format in the online tool that I used (no command lines in the tool). This is the output I have to deal with.

lran2008 · 08-27-2013, 07:22 AM

Quote:

Originally Posted by Rsola

Thank you for your reply, but like I indicated, I can't set the output format in the online tool that I used (no command lines in the tool). This is the output I have to deal with.

Sorry, I didn't notice it. I don't know what's the output format by online blast. But if it can be opened by excel or be imported in to R, you could get what you want then.

GenoMax · 08-27-2013, 07:29 AM

Are you able to use the command line/have access to python? Following may work in that case

https://bitbucket.org/ctb/ngs-course....py?at=default

Extended in this post:

http://haotu.wordpress.com/2012/03/0...-to-csv-excel/

rhinoceros · 08-27-2013, 07:33 AM

I'm not really following how your output is formatted, but I'm sure clever use of e.g. sed could solve your problem. That or using blast_formatter (if your output is asn.1)..

GenoMax · 08-27-2013, 07:35 AM

If you used NCBI to do the search then you can download the results as "hit table.csv" file under the "download" option on the results page.

SDPA_Pet · 08-01-2014, 09:57 AM

Hi GenoMax,

Actually, it is more complicated. The blast output was extracted from MEGAN. It was originally blasted using -m 0 format. I extracted some blast output of some pathways in order to look at the details. I would like to report the highest hit score species in my paper. So, it would be easy for me to convert it to tabular format.

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08-27-2013, 06:52 AM	#1
Rsola Junior Member Location: Europe Join Date: Aug 2013 Posts: 2	Convert Blast output to tabular Hi, Does anybody know how to convert Blast Output as below to a tabular (.csv) output or how to extract top hits? In the online tool that I use I can't select for tabular output. Thanks! Query= OsSNP0002 (142 letters) Database: ../uniprot-oryza-sativa-indica.fasta 42,240 sequences; 15,872,719 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value tr\|A2WJN5\|A2WJN5_ORYSI Putative uncharacterized protein OS=Oryza... 55 2e-18 tr\|B8AKP7\|B8AKP7_ORYSI Putative uncharacterized protein OS=Oryza... 53 6e-17 tr\|B8AEL6\|B8AEL6_ORYSI Putative uncharacterized protein OS=Oryza... 28 1.5 tr\|B8B114\|B8B114_ORYSI Putative uncharacterized protein OS=Oryza... 28 2.0 tr\|B8AQS5\|B8AQS5_ORYSI Putative uncharacterized protein OS=Oryza... 27 2.6 tr\|B8ADP7\|B8ADP7_ORYSI Putative uncharacterized protein OS=Oryza... 27 4.4 tr\|A2ZKU4\|A2ZKU4_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5 tr\|A2Y774\|A2Y774_ORYSI Putative uncharacterized protein OS=Oryza... 26 7.5 tr\|A2WXP8\|A2WXP8_ORYSI Putative uncharacterized protein OS=Oryza... 25 9.7 [/SIZE][/SIZE]

08-27-2013, 06:59 AM	#2
lran2008 Member Location: quebec Join Date: Apr 2013 Posts: 35	You could choose the Blast output format by setting -outfmt. Try -outfmt 6 .

08-27-2013, 07:05 AM	#3
Rsola Junior Member Location: Europe Join Date: Aug 2013 Posts: 2	Thank you for your reply, but like I indicated, I can't set the output format in the online tool that I used (no command lines in the tool). This is the output I have to deal with.

08-27-2013, 07:29 AM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	Are you able to use the command line/have access to python? Following may work in that case https://bitbucket.org/ctb/ngs-course....py?at=default Extended in this post: http://haotu.wordpress.com/2012/03/0...-to-csv-excel/

08-27-2013, 07:33 AM	#6
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	I'm not really following how your output is formatted, but I'm sure clever use of e.g. sed could solve your problem. That or using blast_formatter (if your output is asn.1)..

08-01-2014, 09:57 AM	#8
SDPA_Pet Senior Member Location: US Join Date: Apr 2013 Posts: 222	Hi GenoMax, Actually, it is more complicated. The blast output was extracted from MEGAN. It was originally blasted using -m 0 format. I extracted some blast output of some pathways in order to look at the details. I would like to report the highest hit score species in my paper. So, it would be easy for me to convert it to tabular format.