Re^6: fasta hash

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Re^7: fasta hash by moritz (Cardinal) on Aug 26, 2011 at 19:40 UTC
So, what's your current code? And please indent it properly, and `use strict; use warnings;`. Otherwise I'm not going to comment on it. Perl 6 - second systems done right	[reply] [d/l]
Re^7: fasta hash by Marshall (Canon) on Aug 28, 2011 at 15:32 UTC
Instead of processing the second file line by line, it is possible to use the '>' character as an end-of-line input separator. This simplifies processing of the file. #!/usr/bin/perl -w use strict; open (IDS, '<', "fastaIds") or #with your data 2056360012 2056360013 die "cannot open fastaIds $!\n"; #-------------# my %ids; while (<IDS>) #process first file with only ID's { chomp; $ids{$_}=1; } #-------------# $/='>'; #input record separator is now '>' while (<DATA>) { chomp; # now works on '>' not \n next if /^\s$/; # first record will be blank my ($id) = /^\s(\d+)/; print ">$_" if $ids{$id}; #print all lines for this id } #-------------# =prints > 2056360012 1047627436237 yyyacgagchagshgashcgahcgac acsasasasacsacsasasacaca ascassacsaascascascascac > 2056360013 1047627436238 xxxxcgagchagshgashcgahcgac acsasasasacsacsasasacaca ascassacsaascascascascac =cut __DATA__ > 2056360012 1047627436237 yyyacgagchagshgashcgahcgac acsasasasacsacsasasacaca ascassacsaascascascascac > 2056360013 1047627436238 xxxxcgagchagshgashcgahcgac acsasasasacsacsasasacaca ascassacsaascascascascac [download]	[reply] [d/l]