Extract fasta sequence from multifasta file using id and position in range

Question

[MG_19]

Hi,

I have a multifasta file from which I want to extract sequence based on id and position of sequence in specific range. Please suggest some tool or program that can be useful. My seq file is:

>seq1
ATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCC

>seq2
AACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCT

>seq3
TTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAG

My id file is:

seq1    5   15
seq2    2     10
seq3    10  20

[GenoMax]

Use seqtk (LINK).

seqtk subseq in.fa reg.bed > out.fa

[Fatima]

You can use the following code:

cat id_file.txt | while read id start stop; do echo ">"$id >> output_file.fasta ;  perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw('$id')}print if $c' seq-file.fasta | tail -n +2 | cut -c $start-$stop >> output_file.fasta ; done

To use this code you first need to delete empty lines from your sequence file:

perl -p -i -e "s/^\n$//g" seq-file.fasta

if you don't want to modify the original file, try:

perl -p -e "s/^\n$//g" seq-file.fasta > new_seq-file.fasta

If each of your sequences is one line, you can use this code too:

cat id_file.txt | while read id start stop; do echo ">"$id >> output_file.fasta ;  grep -A 1 ">$id" seq-file.fasta  | cut -c $start-$stop >> output_file.fasta ; done

If you want to add start and stop to the header, you can use this echo instead of echo ">"$id:

echo ">"$id"_"$start"_"$stop

The output:

>seq1_5_15
AGAGCCTTGTC
>seq2_2_10
ACTCAGTTT
>seq3_10_20
CCGTGGAGGAG

[Fatima]

; done was missing from two of my commands. I added them.

[Joe]

You have tagged R, but are asking for any tools. Can you clarify your requirements?