or, if the first array is really a text file, say on a UNIX/LINUX system, you could cat the first file and read it line by line.. no? 
the scanning perl program gen.pl:
---------------------------------
#!/usr/bin/perl
use strict;
my @array = qw(13470319 13470331 15460001 13490216);
my @array2;

while(my $line =  <> ) {
    foreach my $id (0..$#array) {
        $array2[$id]=$line if $line =~  m/^gi\|($array[$id])\|/;
    }
}
print "order: ", join (" ", @array), "\n";
map {print} @array2;
-------------------------------
the text file:
gi|13470331|ref|NP_101896.1| hypothetical protein
MFWVTKKALMPFLMLPAGIIFVSAVGYAINWLFSTLFQFQPPLVEGPAGPVTVLIFTITMLLAYDISYYL
gi|13470319|ref|NP_101897.1| hypothetical protein
MGAYCQAHPACKVTDRTVIGRRDAAMNAPFVLAIPRTRTFEVVTSAARLAEIAPAWTALWQRAGGLVFQH
-------------------------------
the execution:
# cat gen.txt | perl gen.pl
order: 13470319 13470331 15460001 13490216
gi|13470319|ref|NP_101897.1| hypothetical protein
gi|13470331|ref|NP_101896.1| hypothetical protein

[download]

this just looked like a quick and keep it simple job to me..

UPDATE: updated the code to display correct order..

--
to ask a question is a moment of shame
to remain ignorant is a lifelong shame

In reply to Re: retrieving in the correct order by insaniac
in thread retrieving in the correct order by Anonymous Monk

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