Need a practical way to process fasta files with Bio::SeqIO module ? Below code will print sequence id and sequence length with tab per line.
perl -MBio::SeqIO -e '$seq=Bio::SeqIO->new(-fh => \*STDIN);while ($myseq=$seq->next_seq){print $myseq->id,"\t",$myseq->length,"\n";}' < filename
OR
cat filename | perl -MBio::SeqIO -e '$seq=Bio::SeqIO->new(-fh => \*STDIN);while ($myseq=$seq->next_seq){print $myseq->id,"\t",$myseq->length,"\n";}'
There are many more methods to use from Bio::Seq, such as revcom, translate, subseq(start,end), primary_id, desc, etc.
Piped file does not need to be in Fasta format, there are many other formats (listed here) which SeqIO can parse successfully.
UPDATE: If you are using this one-liner in a pipe, you might need to declare the format so that the stream is processed correctly. Also, in order to retrieve Bio::Seq methods, please use “->seq” to access the final sequence.
Considering all these updates, the one-liner should look like this:
perl -MBio::SeqIO -e '$seq=Bio::SeqIO->new(-fh => \*STDIN,-format=>"fasta");while ($myseq=$seq->next_seq){print $myseq->id,"\t",$myseq->length,"\t",$myseq->seq,"\t",$myseq->translate->seq,"\n";}'
