Extract reads from fasta file (specific read_names)and make a new fasta file

Question

[KVC_bioinfo]

Hello all,

I have a huge fasta file. I need to extract few reads from the original fasta file. I have the read names which I want to extract. I want to make a new fasta file from those extracted reads. I am not sure how to proceed with this. Could someone help me here?

Thank you in advance.

Answer 1

[GenoMax]

Use faSomeRecords from Jim Kent's utilities at UCSC.

This also is one of the FAQ's on BioStars, which you should have found by searching:
Extract A Group Of Fasta Sequences From A File
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
Extract Sequence From Fasta File Using Ids From A Separate File

Answer 2

[Joseph Hughes]

First make sure your fasta sequences in sample1.fa are on a singleline rather than warpped around multple lines:

awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa

Then simply grep the identifier/name of the sequence you want and the following line -A 1:

grep -A 1 "idX" sample1_singleline.fa > filtered.fa

If you have multiple identifiers in a file id.txt :

grep -A 1 --no-group-separator -f id.txt sample1_singleline.fa > multiple_filtered.fa

[yeyan.qiu]

Hi Joseph,

I've tried your commands. It worked very well with single identifier/name of the sequence, but there is a problem with extracting multiple identifiers. So, the desired ID was typed in a .txt file, and after running the third command, the result is the same with the input without filtering anything. I wonder it might be something wrong with how I organize the inquiry multiple identifiers in .txt file? Could you please provide one example of the .txt inquiry?

Sincerely,

Yeyan

Answer 3

[Joe]

Here's the script I created to retrieve fasta's by key.

https://github.com/jrjhealey/bioinfo-tools/blob/master/fastafetcher.py

It assumes your list of keys is a simple line separated column of strings.

key1
key2
key3

Then just invoke:

python fastafetcher.py -f myseqs.fasta -k mykeys.txt

NB I've never tested this on very large files, so can't vouch too much for its speed or memory efficiency.

[KVC_bioinfo]

Thank you very much I will try it out

[yeserin]

Hey,

I am trying to use the python code to extract a bunch of sequences from fasta file. I get this warning :

"[yeserin@rackham3 outliers]$ python fastafetcher.py -f myseqs.fasta -k mykeys.txt Traceback (most recent call last): File "fastafetcher.py", line 9, in <module> from Bio import SeqIO ImportError: No module named Bio"

Do I also need to use another module called Bio?

[GenoMax]

You need biopython installed. Use one of the other options above if you can't install that.

[yeserin]

Ah, I found out that not python but biopython works with the code. The problem is solved.