#66 slimmer ncbi_taxa_id crach on gene_association.fb

Seth Carbon

From list; reproduced on dev machine:

I've tried to run the GO slimmer on the file gene_association.fb, downloaded from the GO ftp site. I've used the Generic GO Slim set and have requested a tab-delimited gene association file. I got the following error:

Can't call method "ncbi_taxa_id" on an undefined value at /data/share/goweb/www-data/html/go-dev/amigo/perl/AmiGO/Slimmer.pm line 235.


  • Seth Carbon

    Seth Carbon - 2011-03-12

    Impossible to reproduce by manipulating input or separating parts--had to essentially run everything backwards.

    The error was in the fact that the file type detection package runs the pointer forward, but does not return it when done and exiting, and the position stays there for any further things that work on that filehandle. This caused later things to read the input file with the top clipped off at a very inconvenient spot, ruining any parsing of the input.

    It is now zeroed manually.

  • Seth Carbon

    Seth Carbon - 2011-03-12
    • priority: 6 --> 7
    • status: open --> closed-fixed

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