#updated - trying out new software
!date

!bash5tools.py m130619_081336_42134_c100525122550000001823081109281326_s1_p0.bas.h5.1 --outFilePrefix myreads --outType fasta --readType Raw

!bash5tools.py -h
!wget http://eagle.fish.washington.edu/whale/Pat/Analysis_Results/m130619_081336_42134_c100525122550000001823081109281326_s1_p0.bas.h5
pwd

!wc m130619_081336_42134_c100525122550000001823081109281326_s1_p0.bas.h5.1

!head /Volumes/web/cnidarian/OlyO_Pat_PacBio_10k_contigs.fa

#finished

!makeblastdb -in /Volumes/web/cnidarian/OlyO_Pat_PacBio_10k_contigs.fa -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/OlyO_PacBio_10kcontigs

!blastn -query /Volumes/web/cnidarian/OlyOv3_400bp.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/OlyO_PacBio_10kcontigs -out /Volumes/web/cnidarian/OlyOv3_400_blastn_OlyO10kcontigs -outfmt 6 -evalue 1E-20 -num_threads 2 -task blastn

!head /Volumes/web/cnidarian/OlyOv3_400_blastn_OlyO10kcontigs

!head /Volumes/web/cnidarian/OlyOv3_400bp.fasta

!grep -c "OlyO_Pat_" /Volumes/web/cnidarian/OlyOv3_400_blastn_OlyO10kcontigs 

!2_Blast2gff.pl -i /Volumes/web/cnidarian/OlyOv3_400_blastn_OlyO10kcontigs -o /Users/sr320/Desktop/OlyO10kcontigs_exon_a.gff -d "OlyOv3_400" -p EXON -s "something"

mv /Users/sr320/Desktop/OlyO10kcontigs_exon_a.gff /Volumes/web/cnidarian/

!head /Volumes/web/cnidarian/OlyO10kcontigs_exon_a.gff

!wget https://usegalaxy.org/dataset/display?dataset_id=bbd44e69cb8906b586614e867a9985b1&to_ext=bed

pwd

ls

!/Users/sr320/Dropbox/Steven/gt/fish546/2_Blast2Gff.pl \
-i /Volumes/web/dermochelys/Bioinformatics/IGV\ stuff/otbnos.tab \
-o /Volumes/web/cnidarian/Olytranv2_OlyPacBio_v02.gff \
-d "OlyOvtran_v2" \
-p EXON \
-s "something"

!head /Volumes/web/cnidarian/OlyOv3_400_blastn_OlyO10kcontigs

!head /Users/sr320/Desktop/OlyO10kcontigs_exon_a.gff

!head /Volumes/web/dermochelys/Bioinformatics/IGV\ stuff/otbnos.tab

# could just awk etc "!awk '{ print $10 }'

!head /Volumes/web/cnidarian/Olytranv2_OlyPacBio_v02.gff