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Extraction of best alignment in blast out put

Hey everyone

I have about 4000 blast tab limited output, from thees output I want to extract best alignment (first line only) and want to store another different 4000 files. How is it possible using awk or some other programme

Please help me

perl awk sequence blast
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updated by Ram Ram • written by Eva_Maria Eva_Maria

Hi,

Can you post the first 10 lines or so from your tab limited output?

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written by Tej Sowpati Tej Sowpati 
GCF_000196095n.fasta_2    GCF_001270975n.fasta_3470    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270945n.fasta_718    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270905n.fasta_1870    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270885n.fasta_614    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270825n.fasta_533    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270815n.fasta_2554    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001006105n.fasta_866    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_000975195n.fasta_1323    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_000972045n.fasta_4282    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_000960685n.fasta_1698    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_000958595n.fasta_2383    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_000951795n.fasta_4194    100.00    1362    0    0    1    1362    1    1362    0.0    2516
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updated by Ram Ram • written by Eva_Maria Eva_Maria

output am expecting like this

GCF_000196095n.fasta_2    GCF_001270975n.fasta_3470    100.00    1362    0    0    1    1362    1    1362    0.0    2516
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updated by Ram Ram • written by Eva_Maria Eva_Maria

Caution: there is no 'best' alignment in your example, all alignments you show have equal score, identity, e-value etc. The first one is by no means the best. I don't know what you want to do with the output, but using only the first line is often not a good strategy.

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

Showing some sample data in your hand and how you are expecting the output file would help to figure it out and more importantly 'posting what you have tried so far is a good practice'.

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updated by Ram Ram • written by venu venu

input file

GCF_000196095n.fasta_2    GCF_001270975n.fasta_3470    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270945n.fasta_718    100.00    1362    0    0    1    1362    1    1362    0.0    2516
GCF_000196095n.fasta_2    GCF_001270905n.fasta_1870    100.00    1362    0    0    1    1362    1    1362    0.0    2516

then expected out put

GCF_000196095n.fasta_2    GCF_001270975n.fasta_3470    100.00    1362    0    0    1    1362    1    1362    0.0    2516
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updated by Ram Ram • written by Eva_Maria Eva_Maria

Do you need each of the line in different file? (Please edit your question instead of using comment box)

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written by venu venu

2 answers

you could have simply used head -1

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written by Michael Dondrup Michael Dondrup

i got a awk comment like this

 awk 'NR==1' inputfile > outputfile

this ll work for my problem

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updated by zx8754 zx8754 • written by Eva_Maria Eva_Maria

So, you want only the first line, and then discard the remaining lines? Or, do you want each of your 4000 lines in 4000 different files?

Edit: Never mind. If you got a solution, that's good enough!

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written by Tej Sowpati Tej Sowpati

On a related note, please use professional language. I'd phrase your response so:

Yes, I would like each line in a different file. I used the following awk command to solve my problem: awk 'NR==1' inputfile > outputfile

This works for my case. Thank you for your support.

SMS/IM jargon, typos, improper casing, etc make you look like you're not serious about what you're doing. As another bioinformatician from Chennai, I know the emphasis our folks have on being good at professional communication. Here's to hoping you'll work on this aspect!

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written by Ram Ram

Thank you for your suggestions. I will take everything you have said into consideration.

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written by Eva_Maria Eva_Maria

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