genemapper query wrt swissprot IDs

[rsturm]

Hi Damian,

I'm working with Abacus and would like to report the gene identifiers
in the output. I'm using a swissprot fasta for searching so I need to
have uniprotmapper produce a tab-deliminated file containing the
swissprot IDs rather than uniprot IDs. In cmd line I type the
following:

java -jar uniprotmapper.jar -t human -s

The uniprot_sprot_human.dat.gz is downloaded successfully but when the
script attempts to collect the protein IDs I get the following error:

xception in thread "main" java.lang.NullPointerException
at uniprotMapper.parse_gz(unknown source)
at uniprotMapper.main (unknown source)

Could you assist me in generating the gene map file I am hoping to use
for my abacus searches?

Thanks for the help!

Rob

[GATTACA]

Hi Rob.

It looks like the format of the files that uniprotMapper.jar parses
have changed. This is what's causing the error.
I've fixed the code and uploaded a new version of the program to the
abacus website.

Give it a try and let me know if you have problems.
Thanks for using Abacus.

Cheers,
Damian

[rsturm]

Damian, the new version worked great thanks!

Rob