The code perl -ne "print if /^>/" test.fasta works just quite quickly.

I am reading this file from the same folder that the program is in... While not wanting to resort to a regex to extract the sequences and their header information I believe this is going to be my only way through!

In reply to Re^2: Bioinformatics: Slow Parsing of a Fasta File by Anonymous Monk
in thread Bioinformatics: Slow Parsing of a Fasta File by Anonymous Monk

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