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

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In reply to Re^7: fasta hash by Marshall
in thread fasta hash by morio56

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