from IPython.display import HTML
HTML('<iframe src=http://en.m.wikipedia.org/wiki/Pyura_chilensis width=80% height=350></iframe>')

from IPython.display import HTML
HTML('<iframe src=../fastqc/PiuraChilensis_Coquimbo_fastqc/fastqc_report.html width=100% height=650></iframe>')

from IPython.display import HTML
HTML('<iframe src=../fastqc/PiuraChilensis_Valdivia_fastqc/fastqc_report.html width=100% height=650></iframe>')

from IPython.display import HTML
HTML('<iframe src=../fastqc/trimmer/PiuraChilensis_Coquimbo_trimmer_out_fastqc/fastqc_report.html width=100% height=650></iframe>')

from IPython.display import HTML
HTML('<iframe src=../fastqc/trimmer/PiuraChilensis_Valdivia_trimmer_out_fastqc/fastqc_report.html width=100% height=650></iframe>')

#in repo
!head ../data/Piura_v1_contigs.fa

!blastx \
-query ../data/Piura_v1_contigs.fa \
-db /Volumes/Bay3/Software/ncbi-blast-2.2.29\+/db/uniprot_sprot_r2013_12 \
-out ../data/Piura_v1_uniprot_sprot.tab \
-evalue 1E-05 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
-num_threads 2

#in repo
!tail -2 ../data/Piura_v1_uniprot_sprot.tab

#still needs to be run

!/Applications/bioinfo/ncbi-blast-2.2.30/bin/blastx \
-query ../data/PiuraC_Val_Trinity_2ndhalf.fasta \
-db /Users/sr320/data-genomic/blast/db/uniprot_sprot_r2015_01 \
-out ../data/PiuraC_Val_Trinity_uniprot_sprot_2ndhalf.tab \
-evalue 1E-05 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
-num_threads 6

!tail ../data/PiuraC_Val_Trinity_uniprot_sprot_2ndhalf.tab

!wc -l ../data/Piura_v1_uniprot_sprot.tab

!head -2 ../data/Piura_v1_uniprot_sprot.tab

!tr '|' "\t" <../data/Piura_v1_uniprot_sprot.tab> ../data/Piura_v1_uniprot_sprot_sql.tab
!echo SQLShare ready version has Pipes converted to Tabs ....
!head -1 ../data/Piura_v1_uniprot_sprot_sql.tab