!wget http://eagle.fish.washington.edu/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta

!head /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta

!tail /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta

!tail /Users/sr320/Desktop/0001_DataS1.fa

#confirmed file in question was published on Figshare and MER Notes. 

#not looking good re the word doc and the data.
#will try to blast primers as independant verification

!makeblastdb -in /Volumes/web/cnidarian/Supp_1_Ostrea_lurida_transcriptome.fasta -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/OlyO_transcriptome_v1

#query sequence needs to be primers

!blastn -query /Volumes/web/cnidarian/OlyO_Chi_primers.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/OlyO_transcriptome_v1 -out /Volumes/web/cnidarian/OlyO_Chi_primers_blastn1 -word_size 20 -outfmt 6  

!head /Volumes/web/cnidarian/OlyO_Chi_primers_blastn1

!grep "Ostrea_lur_contig28411" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt

!grep -w "Ostrea_lur_contig402" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt
#need exact mactch to exclude 402X -w

!grep -w "Ostrea_lur_contig2667" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt

!grep -w "Ostrea_lur_contig95" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt

!grep -w "Ostrea_lur_contig16177" /Volumes/web/cnidarian/Supp_3_Ost_lurida_SPIDs.txt