So my entire project is to use LIBSVM to predict a protein's function. What I have been doing, is taking the Protein database's list of protein numbers (accession numbers, the 6 digit things) and matching them to their PF numbers, which is in what PF groups. The two files i have been using are up there. Now I have managed to get the data in the following format:

B3T3Y0 | PF02517.11
B3T4D5 | PF13371.1 PF13369.1
B3T4G0 | PF13607.1
B3T516 | PF08438.5
B3T517 | PF13207.1 PF13238.1
B3T644 | PF14382.1
B3T662 | PF13248.1
B3T663 | PF13248.1 PF13248.1 PF13240.1

[download]

which is what i actually wanted all along. Thanks Count Zero. What i don't know is what to do to put it into LIBSVM, but my groupmate is looking into that. Thanks everyone though!

In reply to Re^2: Making a hash with groups of IDs by jemswira
in thread Making a hash with groups of IDs by jemswira

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