Hi, please bear with me as I'm new to Perl. I have two arrays: one is a list of full gene names (GI), and one is a list of just their accession numbers (Accession). It looks like:

my @GI = ("\Qgi|Q384722390|emb|WP_938420210.1|Gene name\E","\Qgi|34254
+6780|emb|WP_934203412.1|Gene name\E");
my @Accession = ("WP_938420210.1","WP_934203412.1");

[download]

That is only an abbreviated example. In the real program, the GI list is much longer because it contains all the genes, and the Accession array only contains the Accession numbers of the ones I'm interested in. The Accession numbers are part of the GI full name, so I thought I could use a regular expression to go through each element of the arrays and find matches for the 469 accession numbers, like this: 

 my $X = 0;
my $Y = 0;
while($X <= 468){ 
    if(/$Accession[$X]/ =~ $GI[$Y]){
        print $GI[$Y];
        $X = $X + 1;
        $Y = 0;
                                                      }
    else{$Y++};
                             }

[download]

However, when I do this, I get the error "Use of uninitialized value in pattern match (m//) and also use of uninitialized value within @GI in regexp compilation. Does anyone know what I am doing wrong? Thank you!

In reply to Using regular expressions with arrays by andybshaker

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.