#tab-delited fasta
!date

!head /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa

!sed 's/Roberts_20100712_CC_F3_trimmed_/BlackAbalone_v3_/g' </Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa> /Volumes/web/cnidarian/lft_BlackAbalone_v3_fasta.fa
#sed 's/abc/XYZ/g' <infile >outfile


!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_fasta.fa

!grep -c ">" /Volumes/web/cnidarian/lft_BlackAbalone_v3_fasta.fa


!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout

#now with version28
!blastx -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/swissprot -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_tax1 -outfmt "6 std stitle staxids sscinames scomnames sblastnames" -evalue 1E-10 -max_target_seqs 1 

#Updating July 24, 2013
#Want to GOslim pie the transcriptome based on Swiss-Prot
#tr ',' "\t"

!tr '|' "\t" </Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout> /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_b


!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_b

#also need to get rid of version # on Swiss-Prot ID
#note that it will also break bitscore 
!tr '.' "\t" </Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_b> /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_c

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_c

!sed 's/Roberts_20100712_CC_F3_trimmed/Haliotis_cra_v3/g' </Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_c> /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d
#sed 's/abc/XYZ/g' <infile >outfile


!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d

!wc /Volumes/web/cnidarian/lft_BlackAbalone_v3_swissprot_blastout_d

#lets try again to see if can commandline up to SQLShare
!cd /Users/sr320/pythonclient/tools

#cp samtools /usr/local/bin
!cp uploadone.py /usr/local/bin

#SQLShare direct.


!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -d "[sr320@washington.edu].[lft_BlackAbalone_v3_SP_GO_pathway]" -f tsv -o /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt


!head -2 /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt

!wc /Volumes/web/cnidarian/lft_BlackAbalone_sp_go_path.txt

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim.csv

!wc /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim.csv

#query with no evalue limit to verify accuracy
!head /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim_jp.csv

!wc /Volumes/web/cnidarian/lft_BlackAbalone_v3GOslim_jp.csv
wwcd - (verified again in exhell)
#will try the R
%pylab inline

import numpy as np
import matplotlib.pylab as plt

import rpy2
1210 IDs
!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nr_blastout

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_nr_blastout

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_nr_blastout

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa1

!blastn -help
!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/Bay3/CLC_blastdatabases/nt -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa2 -outfmt "6 std stitle staxids sscinames scomnames sblastnames" -evalue 1E-10 -max_target_seqs 1 -task blastn
!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa2
GENE DESCRIPTION AND Tax IDs produced
!sed 's/Roberts_20100712_CC_F3_trimmed_/BlackAbalone_v3_/g' </Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa2> /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa3
#sed 's/abc/XYZ/g' <infile> outfile

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_nt_blastout_taxa3
SELECT 
 id,
 foldchange,
 pval,
 de.Column3 as SPID,
 evalue,
 Column13 as NCBI_nt_Des
  
  FROM [lisa418@washington.edu].[BlkAb_DESeq_SPID]de
  left join [sr320@washington.edu].[lft_BlackAbalone_v3_nt_blastout_taxa3]lft
  on
  de.id = lft.Column1
SELECT 
 id,
 foldchange,
 pval,
 Column13 as NCBI_nt_Des
  
  FROM [lisa418@washington.edu].[BlackAB_DESeq.txt]de
  left join [sr320@washington.edu].[lft_BlackAbalone_v3_nt_blastout_taxa3]lft
  on
  de.id = lft.Column1​
@fu Try to get taxID from SP blast 
!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout

!head /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout

!tail /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout

!grep -c "Roberts" /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout

#running blackAb versus other Abalone at 1e-20

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_ruf_blastout -outfmt 6 -evalue 1E-20 -max_target_seqs 1 -num_threads 2 -task blastn

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_midae_franchini -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_midae_blastout_b -outfmt 6 -evalue 1E-20 -max_target_seqs 1 -num_threads 2 -task blastn

!blastn -query /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_kam_transcriptome -out /Volumes/web/cnidarian/lft_BlackAbalone_v3_Hal_kam_blastout_b -outfmt 6 -evalue 1E-20 -max_target_seqs 1 -num_threads 2 -task blastn

!head /Volumes/web/cnidarian/OrthDB_meta_Lotgi1.fa

!fgrep -c ">" /Volumes/web/cnidarian/OrthDB_meta_Lotgi1.fa

!makeblastdb -in /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/BlackAbalone_Contigs_v3

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/BlackAbalone_Contigs_v3 -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt -max_target_seqs 1 -num_threads 2 -evalue 1E-10

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/BlackAbalone_Contigs_v3 -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt -max_target_seqs 1 -num_threads 3 -evalue 1E-20

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

#wc       Print byte, word, and line counts
!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt

!fgrep -c "Roberts_20100712_CC" /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn.txt

!fgrep -c "Roberts_20100712_CC" /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_BlackAb_v3_tblastn_b.txt

#-A is the number of lines After
!fgrep -A 10 "Roberts_20100712_CC_F3_trimmed_contig_3682" /Volumes/web/cnidarian/BlackAbalone_Contigs_v3.fa

#in the meantime will blast other Haliotis databases

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_kam_transcriptome -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt -max_target_seqs 1 -num_threads 1 -evalue 1E-20

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_midae_franchini -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt -max_target_seqs 1 -num_threads 1 -evalue 1E-20

!makeblastdb -in /Volumes/web/cnidarian/H.rufescens_contig.fa -dbtype nucl -out /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome

!tblastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OrthDB_meta_Lotgi1.fa -db /Volumes/web/whale/fish546/blast/db/Haliotis_rufescens_transcriptome -outfmt 6 -out /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt -max_target_seqs 1 -num_threads 1 -evalue 1E-20

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_kam_tblastn.txt

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_midae_franchini_tblastn.txt

!head /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt

!wc /Volumes/web/cnidarian/OrthoDB_Lotgi1_Haliotis_rufescens_tblastn.txt