#unzipping  [-]x --extract --get;  -v, --verbose; -z, --gzip; -f, --file F
!tar -xzvf  ncbi-blast-2.2.29+-universal-macosx.tar.gz

cd ncbi-blast-2.2.29+/bin



ls -1

#check to see if "works"
!blastx -h

cd ncbi-blast-2.2.29+/

cd db

ls

!gzip -d uniprot_sprot.fasta.gz

ls

pwd

#note I am working in dir db, thus can just use file names. Most times you might use the complete path.
!makeblastdb -in uniprot_sprot.fasta -dbtype prot -out uniprot_sprot_r2013_12 

#creating new directory; 
!pwd

cd ..

!mkdir query

cd query/

#getting file from url to local location
#also curl -O works
!wget http://eagle.fish.washington.edu/cnidarian/Ab_4denovo_CLC6_a.fa

#lets get a preview
!head Ab_4denovo_CLC6_a.fa

#word count
!wc Ab_4denovo_CLC6_a.fa

#how many sequences? lets count ">" as we know each contig has 1
!grep -c ">" Ab_4denovo_CLC6_a.fa

#will use full paths..
!blastx \
-query /Volumes/Bay3/Software/ncbi-blast-2.2.29\+/query/Ab_4denovo_CLC6_a.fa \
-db /Volumes/Bay3/Software/ncbi-blast-2.2.29\+/db/uniprot_sprot_r2013_12 \
-out /Volumes/Bay3/Software/ncbi-blast-2.2.29\+/out/Ab_4denovo_CLC6_a_uniprot_blastx.tab \
-evalue 1E-20 \
-max_target_seqs 1 \
-outfmt 6

!head /Volumes/Bay3/Software/ncbi-blast-2.2.29\+/out/Ab_4denovo_CLC6_a_uniprot_blastx.tab

!wc /Volumes/Bay3/Software/ncbi-blast-2.2.29\+/out/Ab_4denovo_CLC6_a_uniprot_blastx.tab