|Perl Monk, Perl Meditation|
Loading only portions of a file at any given timeby TJCooper (Beadle)
|on Nov 30, 2017 at 13:23 UTC||Need Help??|
TJCooper has asked for the
wisdom of the Perl Monks concerning the following question:
I currently load a FASTA formatted file, which contains DNA sequence separated by headers denoted by '>' i.e.:
via bioPerl (Bio::SeqIO), and store the entire FASTA file into memory as a hash:
Or I could code it manually (which is likely quicker given the amount of overhead in Bio::SeqIO).
Based on a second input file, I then subsample the FASTA sequences and do some processing.
Each line of $IN2 includes the header from its associated FASTA sequence.
This works fine, and on modern computers the memory usage isn't too much of a problem even with larger genomes (Human etc.). Nevertheless, i'd like to take advantage of the fact that my second input file ($IN2) is always sorted by header and thus, for example, the first 5000 lines of it only need the FASTA sequence from >header1. This could potentially save me having to load the entire FASTA file into memory and instead only load the sequence that is currently being used.
I'm however having a tough time trying to figure out how to actually do this so any suggestions or code would be greatly appreciated.