[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

I've patched ISF to correct for this misbehavior.  The patch is  
listed below.

-Aaron

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 5. 98198.txt
> It did not find the name of the table taxonomy (the taxonomy table  
> was updated but the error persist)
> The 98198.gb is an example

Index: InsertSequenceFeatures.pm
===================================================================
--- InsertSequenceFeatures.pm   (revision 4572)
+++ InsertSequenceFeatures.pm   (working copy)
@@ -872,14 +872,18 @@
    my $species = $bioperlSeq->species();
    my $sciName;
    if ($species) {
-    $sciName = $species->genus() . " " . $species->species();
+    # for exotic taxa, common name is more likely to match in NCBI
+    # Taxonomy than whatever BioPerl guesses the genus/species names
+    # to be:
+    $sciName = $species->common_name();
    } else {
      $sciName = $self->getArg('defaultOrganism');
      if (!$sciName) {
        my $acc = $bioperlSeq->accession_number();
        $self->userError("Sequence '$acc' does not have organism  
information, and, you have not supplied a --defaultOrganism argument  
on the command line");
      }
-    $sciName =~ /\w+ \w+/ || $self->userError("Command line argument  
'--defaultOrganism $sciName' is not in 'genus species' format");
+    # this is an invalid assumption, e.g. 'Blastocrithidia sp. ex  
Triatoma garciabesi':
+    # $sciName =~ /\w+ \w+/ || $self->userError("Command line  
argument '--defaultOrganism $sciName' is not in 'genus species'  
format");
    }
    return $self->getIdFromCache('taxonNameCache',