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In Blast+, How Can I Ignore The *** No Hits Found *** In Output

Hi,

Doing a blast+, using the default output ( -outfmt 0 ), there is a way to not save all the queries that doesn't hit ?

I want to eliminate from output the lines around No hits found , I think it's not hard to do this using python against the blast+ output, but if the program itself has a native option to do that, it would save a considerable amount of time/processing and space.

Just to be crystal clear, that is the part I want to expunge from output:

Query= FCC1WLUACXX:8:1306:8508:25826#GAACGTGA/1

Length=100


***** No hits found *****



Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 8650833807

Thank you all in advance.

blast+
• 6,371 views • link
updated by Biostar Biostar • written by commonsnook • commonsnook

i don't know if you can fix that by parameter settings. but you can probably pipe the blast output through a custom utility to cut off the empty output (you can iterate over hits in BioPerl) and then to zip the stream in order to save some space.

• 0 views • link
written by Pavel Senin Pavel Senin

That was the solution I ended up using, I reduced my output from 2.8gb to 1.8gb using a python script. Sadly it took a few extra time to process, something like 620 minutes VS 640 minutes.

• 0 views • link
written by commonsnook • commonsnook

Do you need the standard BLAST output? If not, choose one of the other output formats (e.g. tabular), where only hits are reported. Otherwise, you'll need a parser, which exists in (Bio)Python and many other languages.

• 475 views • link
written by Neilfws Neilfws

if you have a huge dataset you may produce both outputs, thedefault one and in a tabular format, you may use tabular one to make analysis and a standard one to see alignments etc

• 0 views • link
written by User000 User000

Is it possible to filter the standard BLAST output since then?

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written by bird77 • bird77

1 answer

As far as I know one cannot modify the standard Blast output.

The reasons for it looking the way it is are largely historical but since so many tools rely on parsing this exact format they had to maintain it identical over a decade .

• 236 views • link
written by Istvan Albert Istvan Albert

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