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t/IO_psi10.t  view on Meta::CPAN

my @components = $g1->connected_components;
is scalar @components, 2;

# there was an intermittent bug in articulation_points() here
# but not in the invocation above, this appears to be fixed
# in Graph v. .86
@rts = $g1->articulation_points;
is scalar @rts, 1;
@proteins = $rts[0]->proteins;
$seq = $proteins[0];
is $seq->desc, "Erythropoietin receptor precursor";

#
# GO terms
#
$n = $g1->get_nodes_by_id("EBI-474016");
@proteins = $n->proteins;

#
# PSI XML from HPRD
#

t/data/bovin_small_intact.xml  view on Meta::CPAN

             <names>
               <shortLabel>rat</shortLabel>
               <fullName>Rattus norvegicus</fullName>
             </names>
           </organism>
           <sequence>MTAAENVCYTLINVPMDSEPPSEISLKNDLEKGDVKSKTEALKKVIIMILNGEKLPGLLMTIIRFVLPLQDHTIKKLLLVFWEIVPKTTPDGRLLHEMILVCDAYRKDLQHPNEFIRGSTLRFLCKLKEAELLEPLMPAIRACLEHRHSYVRRNAVLAIYTIYRNFENLIPDAPELIHDFLVNEKDASCKRNAFMMLIHADQDRALDYLSTCIDQVQTFGDILQLVIVE...
         </proteinInteractor>
         <proteinInteractor id="EBI-307814">
           <names>
             <shortLabel>cd5r1_bovin</shortLabel>
             <fullName>Cyclin-dependent kinase 5 activator 1 precursor</fullName>
           </names>
           <xref>
             <primaryRef db="uniprotkb" id="Q28199" secondary="cd5r1_bovin" version="SP_48"/>
             <secondaryRef db="interpro" id="IPR004944" secondary="CDK5_activator"/>
             <secondaryRef db="uniprotkb" id="Q28865" secondary="cd5r1_bovin" version="SP_48"/>
             <secondaryRef db="uniprotkb" id="Q29462" secondary="cd5r1_bovin" version="SP_48"/>
             <secondaryRef db="intact" id="EBI-307814" secondary="cd5r1_bovin"/>
           </xref>
           <organism ncbiTaxId="9913">
             <names>

t/data/sv40_small.xml  view on Meta::CPAN

             <names>
               <shortLabel>mouse</shortLabel>
               <fullName>Mus musculus</fullName>
             </names>
           </organism>
           <sequence>MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEALRVSGAPAAQDPVTETPGPVAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVMCTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCSDGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTI...
         </proteinInteractor>
         <proteinInteractor id="EBI-617321">
           <names>
             <shortLabel>epor_human</shortLabel>
             <fullName>Erythropoietin receptor precursor</fullName>
           </names>
           <xref>
             <primaryRef db="uniprotkb" id="P19235" secondary="epor_human" version="SP_48"/>
             <secondaryRef db="go" id="GO:0005887" secondary="C:integral to plasma membrane"/>
             <secondaryRef db="go" id="GO:0004900" secondary="F:erythropoietin receptor acti"/>
             <secondaryRef db="go" id="GO:0007165" secondary="P:signal transduction"/>
             <secondaryRef db="interpro" id="IPR002996" secondary="Cytkn_recept_B/G"/>
             <secondaryRef db="interpro" id="IPR009167" secondary="EPO_receptor"/>
             <secondaryRef db="interpro" id="IPR003961" secondary="FN_III"/>
             <secondaryRef db="interpro" id="IPR008957" secondary="FN_III-like"/>