[Bioperl-l] Sporadic Failure to retrieve Sequence Objects from GenPept

Warren Gallin wgallin at ualberta.ca
Fri Mar 17 17:48:33 EST 2006


	I am getting a sporadic error running a script.  The code fragment  
that is failing is

	foreach $gi (@ginumbers){
		$find_gi = $gi;
		$find_gi =~ s/gi(\d+)/"$1"/;
		$seq_object = $database -> get_Seq_by_id("$find_gi");
		$description = $seq_object -> desc;      #line 54
		$species_object = $seq_object -> species;
		$species_name = $species_object -> binomial;

It is returning a message like this, although the gi number that it  
fails on varies from run to run.

-------------------- WARNING ---------------------
MSG: id ("73998177") does not exist
Can't call method "desc" on an undefined value at gi_to_name.pl line 54.

As far as as I can tell, every once and awhile the retrieval of  
$seq_object from the database (GenPept in this case) is failing.

The gi numbers exist, and if I just run the script again it doesn't  

This leads me to believe that there may be some kind of internal wait  
cycle that returns undefined if the $seq_object retrieval has not  
completed in a certain time.

In any case, is there some way to tweak a script to prevent this kind  
of problem?


Warren Gallin

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