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Jit answered the question What is Bioinformatics ?- BioHack has a new avatar
- Jit created a new bio-script Compress and decompress the sequence with perl
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- Abhimanyu Singh created a new bio-script Extract fasta sequence from a multifasta file with fasta header IdsComments
- Rahul Nayak 2114 days ago
perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.fileIf you have a large number of sequences that you want to extract, then you most likely have the sequence identifiers in a separate file. Assuming that you have one sequence identifier per line in the file ids.file, then you can use this one line:
perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file
