#remove newlines
awk '{if (substr($0,1,1)==">"){print "\n"$0} else printf("%s",$0);p++;}END{print "\n"}' DR_091_Mobl_MOE_assembled.fasta > joined.fasta

If I try running BLASTALL with my transcriptome data as the database, I get this error:

[blastall 2.2.22] ERROR: SeqPortNew: lcl

All the names of the sequences are too similar so I have to rename them--I am just going to rename them by number.
awk '/^>/{print ">" ++i; next}{print}' < DR_091_Mobl_MOE_assembled.fasta > renamed_DR_091_Mobl_MOE_assembled.fasta

#export the path the blast
export PATH=$PATH:/Users/laurelyohe/blast-2.2.22/bin/

#format the database 

#because the transcriptome is bigger than the indices, it will serve as the database

formatdb -i renamed_DR_091_Mobl_MOE_assembled.fasta -o T -p F

#run blast

blastall -p tblastx -d renamed_DR_013_Mored_MOE_assembled.fasta -i OR_VR_indices.fasta -e 1e-06 -v 5 -b 5 -a 2 -o ./DR_013_Mored_MOE_assembled_v_OR_VR_indices.tblastx

#now we need to parse the BLAST script

perl ~/Scripts/parse_bls.pl --i DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx > DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx.parsed

#next combine the parsed file with the sequences

~/Scripts/extract_hsps_new.pl -i renamed_DR_091_Mobl_MOE_assembled.fasta -t DR_091_Mobl_MOE_assembled_v_OR_VR_indices.tblastx.parsed -s DR_091_Mormoops_blainvelli