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Since gi and ref seems to be always there, perhaps another suggestion:
perl -pe 's/\|?(?:\s+gi|ref)?\|\s*/\t/g' file

Output:

TRINITY_DN17272_c0_g1_i1 242003970 XP_002422928.1 ...

If you columns are fixed, then perhaps you could:-tab=$(printf "\t")
tr '|' "$tab" < input_file | cut -d "$tab" -f1,3,5,7-

Does that help? What I'm trying is to convert every | to a tab and then...

Hi Corona688,

The OP requires more than just substituting every pipe symbol for a tab.

A less brute-force method:
tr '|' '\t' < infile > outfile

perl -pae '$F[1] = join "\t", (split /\|/, $F[1])[1,3] and $_ = join "\t", @F' BioBing.example

Your target field separator is not clear - do you want the two elements to be each a field of its own with a <TAB> between them, or both making up one field, separated by a space or two?
For the...