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Extract Sequence From Fasta File Using Ids From a separate txt File in linux

Hi everyone,

I have two files a fasta file and a txt file containing a list of sequence ID.

I would like to exclude the list of sequence ID ( text file) from fasta file. I have tried this command : 

seqtk subseq input.fasta list_ids.txt > output.fasta

But it gives me an output with a fasta file containing only the list ofID sequences . I want a output ( fasta) without the sequence ID. if you could explain any answers in detail, I would be highly grateful

rna-seq
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updated by h.mon h.mon • written by roberta.berezin • roberta.berezin

This question has been asked a gazillon times on biostars.org . What did you find so far ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Pierre, i saw similiar questions.. but most of them are about a " different output".. i want a output without the list of ID... I saw a command line in seqtk, pyton, and someothers, but none of them worked for what i want. do u have another alternative ?

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written by roberta.berezin • roberta.berezin

Using seqtk and unix tools:

grep ">" input.fasta | tr -d ">" | grep -v -w -f list_ids.txt > list_ids_2.txt
seqtk subseq input.fasta list_ids_2.txt > output.fasta

Or in one line:

seqtk subseq input.fasta $(grep ">" input.fasta | tr -d ">" | grep -v -w -f list_ids.txt) > output.fasta

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written by h.mon h.mon

2 answers

faSomeRecords from Kent Utilities is the one you want. Linux version linked here, macOS available.

faSomeRecords in.fa listFile out.fa
options:
   -exclude - output sequences not in the list file.
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written by GenoMax GenoMax

As others have said, this has been asked many many times, but this script will also do what you want if you invoke it with --invert.

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written by Joe Joe

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