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Article:
  Relational Modeling of Biological Data: Trees and Graphs
Subject:   fetch() without execute() error in Example 1
Date:   2003-06-15 11:49:37
From:   anonymous2
Response to: fetch() without execute() error in Example 1

Aaron generously offered a solution via email:


In the script, replace the following line:


while(my ($id) = $children->fetchrow_array) {

With this:


for my $row (@{$children->fetchall_arrayref}) {
my ($id) = @$row;


Thanks, Aaron!

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Showing messages 1 through 2 of 2.

  • fetch() without execute() error in Example 1
    2004-01-11 11:31:44  anonymous2 [View]

    It took several days(more than a week) on a pentium-4 freebsd machine to run this code for entire ncbi taxonomy. Is there anything I should check with my MySql or table structure? I have indexed the taxon_id and the parent_id.
    • fetch() without execute() error in Example 1
      2006-02-06 10:55:01  Aaron Mackey | [View]

      The $children statement needs an additional clause, as follows:


      my $children = $dbh->prepare("SELECT id
      FROM taxon
      WHERE parent_id = ?
      AND id <> parent_id");