Filter sequences by ID and copy to a new file

Question

[bionewbie]

Hi,

I'm really new to bioinformatics and I have a large file with sequences. I only need specific sequences for my analysis. How can I filter them by accession number?

thanks!

Answer 1

[Fatima]

If your sequences are only one line you can use this command:

cat IDs.txt | while read line ; do grep -A 1 "${line}" inputfile.fasta >> outputfile.fasta ; done

This command only works when accession numbers do not overlap. Also, please make sure IDs.txt doesn't have any empty lines. And, each line in IDs.txt should have one and only one Accession number, with no extra space.

If your sequences are multi-liner you can convert them to a one-liner fasta file first and then use the above command:

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' <  file.fasta >> inputfile.fasta

When IDs overlap, --perl-regex and $ or \t or other delimiters can be added (depending on the format of the header)

grep -A 1 --perl-regex "${line}$"

grep -A 1 extracts the line containing the pattern, and the line after that

[bionewbie]

In this line, which file is meant to be "file.fasta"? The output file?

   awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' <  file.fasta >> inputfile.fasta

[GenoMax]

file.fasta is your input file.

[Fatima]

Yes, I called the output file inputfile.fasta, because it will be used as input in the other command.

Answer 2

[GenoMax]

Use this solution: C: How do I extract Fasta Sequences based on a list of IDs?