Hi I would like to extract subsequences from a large fasta file and make a new fasta file with the extracted seqences using python preferably.
I have a csv file with the following format:
id, start, stop, header id1, 3, 10, Contig0 id2, 12, 25, Contig1 id3, 19, 40, Contig2
the input fasta file has the following format:
>Contig0 (Contig0 sequence) >Contig1 (Contig1 sequence) >Contig2 (Contig2 sequence)
I would like an fasta file output that has the following format:
>id1 (Contig0 sequence from bp 3-10) >id2 (Contig1 sequence from bp 12-25) >id3 (Contig2 sequence from bp 19-40)
If anyone has any suggestions or a script that can do this, any help would be greatly appreciated.