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How to extract sub fasta sequences from a multiline fasta file ?

Hi

Multiline fasta 
>data1
AADFGHJKASDFG
ASDFGHJKLFGHJK
ZXCVBNMMMMM
>data2
POIUYTREWPOIU
LKJHGFDSSALKJH
MNBVCXZLKJHGF
>data3
QWERTYUIOQWE
ERTYUIRTYUITYUI
ASDFGHJSDFGHS

Interested in extracting only >data2 sequence into text file.

>data2
POIUYTREWPOIU
LKJHGFDSSALKJH
MNBVCXZLKJHGF

Using file option that I'd great. I had a 1000's of ID's in a text file. I tried using grep commands able to extract only 1 line.

 >data2
    POIUYTREWPOIU

Help!

rna dna
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written by sunnykevin97 sunnykevin97

1 answer

how to filter a fasta file with seqs ID

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written by GenoMax GenoMax

Its not working, generates an empty file.

faSomeRecords fsd.fa mfsd.txt out.fa

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written by sunnykevin97 sunnykevin97

You need to list plain fasta header names one per line in mfsd.txt. There can be no > in listing.

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written by GenoMax GenoMax

Other than faSomeRecords is their any tools that can do the same ? Actually it doesn't have append(>>) option. That doesn't solve my problem yet. Help!

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written by sunnykevin97 sunnykevin97

What do you mean it does not have append option? All selected sequences should be in out.fa. If you are doing this for different datasets, just cat output files together. cat out1.fa out2.fa > final.fa.

You need to improvise (especially if you are not a programmer yourself) when needed. You will rarely find tools that do exactly what you need since you may be the only person needing a tool that works like that.

• 0 views • link
written by GenoMax GenoMax

I tried the same, it worked.

Thanks

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written by sunnykevin97 sunnykevin97

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