#make Anaplasma BLAST database
#check source fasta file for number of sequences
#by counting the number of greater-than symbols ('>') in the file, since each
#sequence entry is preceeded by a '>'.
!awk '/>/ { count++ } END { print count }' /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/AnaplasmaGBnt20140305.fasta

#make the Anaplasma BLAST database
#put the "time" command at the beginning for fun
#the "time" command is NOT part of the BLAST package, but is already built into the Terminal
!time makeblastdb -dbtype nucl -in /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/AnaplasmaGBnt20140305.fasta -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/AnaplasmaGBnt20140305

#check cowdria fasta file numbers
!awk '/>/ { count++ } END { print count }' /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/CowdriaGBnt20140305.fasta

#make cowdria BLAST database
!time makeblastdb -dbtype nucl -in /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/CowdriaGBnt20140305.fasta -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/CowdriaGBnt20140305

#check ehrlichia fasta file numbers
!awk '/>/ { count++ } END { print count }' /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/EhrlichiaGBnt20140305.fasta

#make ehrlichia BLAST database
!time makeblastdb -dbtype nucl -in /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/EhrlichiaGBnt20140305.fasta -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/EhrlichiaGBnt20140305

#perform BLASTN of de novo assembly of all abalone seqs
#against anaplasma BLAST database
!time blastn -db  -task blastn -query /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/queries/AllAbDenovo7118contigs.fa -outfmt "6 stitle std" -max_target_seqs 3 -num_threads 16 -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/outputs/AllAbDenovo7118contigsAnaplasmaGBntBLASTN.txt
All BLASTs will be performed in the same fashion with the following options utlized:
-task blastn: Tells BLAST to use BLASTn instead of the default MegaBLAST
-outfmt "6 stitle std": Specifies the output format number 6 (which is a tab-delimited ouput file) and indicates that the output should add the subject title (stitle) in addition to the standard (std) BLASTn output columns.
- max_target_seqs 3: Tells BLAST to match a maximum of 3 database sequences per query sequence.  The default is 500!
- num_threads 16: Speciifies the number of processing threads to use.  I just multiplied the number of CPUs I have listed in my resource monitor by four, since the processor is listed as a quad core.  
#forgot to specify BLAST db
!time blastn -db /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/AnaplasmaGBnt20140305 -task blastn -query /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/queries/AllAbDenovo7118contigs.fa -outfmt "6 stitle std" -max_target_seqs 3 -num_threads 16 -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/outputs/AllAbDenovo7118contigsAnaplasmaGBntBLASTN.txt

#perform BLASTN of de novo assembly of all abalone seqs
#against cowdria BLAST database
!time blastn -db /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/CowdriaGBnt20140305 -task blastn -query /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/queries/AllAbDenovo7118contigs.fa -outfmt "6 stitle std" -max_target_seqs 3 -num_threads 16 -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/outputs/AllAbDenovo7118contigsCowdriaGBntBLASTN.txt

#perform BLASTN of de novo assembly of all abalone seqs
#against ehrilichia BLAST database
!time blastn -db /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/dbs/EhrlichiaGBnt20140305 -task blastn -query /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/queries/AllAbDenovo7118contigs.fa -outfmt "6 stitle std" -max_target_seqs 3 -num_threads 16 -out /home/samb/BioinformaticsTools/ncbi-blast-2.2.29+/outputs/AllAbDenovo7118contigsEhrlichiaGBntBLASTN.txt