#Contigs from Assembly
!head /Volumes/web/cnidarian/SeaStar_transc_v2.fa

#Making the query look better
!sed 's/3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)/Phel_clc/g' </Volumes/web/cnidarian/SeaStar_transc_v2.fa> /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa

!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa

!fgrep -c ">" /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa

#IMPORTANT the location of files will change depending on your computer
!blastx \
-query /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa \
-db /Users/Shared/data/blast/db/uniprot_sprot \
-out /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_1.tab \
-outfmt 6 \
-num_threads 8 \
-max_hsps 1 \
-max_target_seqs 1 \
-evalue 1E-20

!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_1.tab

!tr '|' "\t" </Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_1.tab> /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_sqlready.tab

!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_clc_blastx_uniprot_sprot_sqlready.tab