$ perl -lne 'sub prt{@c && print scalar @c,"\n",join ", ",@c;@c=();print} />/?prt:push @c,$_}{prt'  TheFileName

##</code><code>##

>05143_African_trypanosomiasis
4
TRINITY_DN26760_c1_g1, 18169, 42987, 42987
>05145_Toxoplasmosis
7
43736, 38319, 38320, 38320, TRINITY_DN24151_c3_g1, TRINITY_DN25493_c0_g1