quick links
file="/Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_b.fasta"
!perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_b.fasta > /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414.tab
Converted 206388 FASTA records in 2488079 lines to tabular format Total sequence length: 138128102
!head {file}
>gi|318053987|gb|FQ662477.1|FQ662477 FQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence GGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTA CAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTT ATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAG ATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACA ATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCC TACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATA AAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGAT TAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATT ATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTT
!fgrep -c "AM863560" {file}
1
#Translate pipes to tab so SPID is in separate column for Joining
!tr '|' "\t" </Volumes/web/cnidarian/Cgigas_EST_NCBI_040414.tab> /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab
spd="/Users/sr320/sqlshare-pythonclient/tools/"
#uploading to SQLSHARE
!python {spd}singleupload.py -d Cgigas_EST_NCBI_040414_cl /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab
processing chunk line 0 to 122527 (0.58825802803 s elapsed) pushing /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab... parsing 54E9735E... processing chunk line 122527 to 206388 (163.788265944 s elapsed) pushing /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab... parsing 7C0B8204... finished Cgigas_EST_NCBI_040414_cl
!python {spd}fetchdata.py -s "SELECT * FROM [sr320@washington.edu].[GPL11353_array]ar left join [sr320@washington.edu].[Cgigas_EST_NCBI_040414_cl]est on ar.GB_ACC=est.Column5" -f tsv -o /Volumes/web/cnidarian/GPL11353_fasta.tab
!head -2 /Volumes/web/cnidarian/GPL11353_fasta.txt
ID Row Col ProbeName ContigName GB_ACC Description SEQUENCE Column1 Column2 Column3 Column4 Column5 Column7 43070 507 60 CUST_23696_PI419289827 FP010368.p.cg.6 FP010368 GCAGGCTTACATTTGTTATAACTTGGTGAGGATGGTAAAGGGAAGGTTAGTGTATATTTT gi 260935343 gb FP010368.1 FP010368 GGGCAGAGATTTCAGTGACTTTGAAGTTAAAACAAAATTTTCTTCGGACACTGTGACACTAATGATTTATGTCTTTGTGTTTATATTAACAATTTTATAACAATACCTCAATATCTTATTCAAGATATTTCGGTTTTGGGGTGGGGGGAGTGTGATAGGATTATATTTATCATGATCACATGAAAAGCACATGTTCGTCTATAGCTTTAAGCAAAACGTAACGATAAATATGATTGGTTGTACTTGTACTCGTTTAATTTACATTCGGAAAGTGTCGGTGTCATTCATAATAATTTGGGAAAATGCTGGTTTGAGTTATAAATACATATAGTCGTTCTGATTGGTTAAGAGAAACACACCCCCAGAGCGCGGTGTATACAAAGTCAGGATTTGCCTTAGTCCGGCAGTTGACGTGGAATCTTCTCTAAGGTTCGAGTCAACTCACTTCCCCGGGTAGATGGGTGGGCCCCAGTCTCCATTTCCCGTCTCGTTCATCGTCTCGCTAAGTGTTTTGTTTATTGTCCTGTAAATGTCCATTGTGCAGCATGCTAGGCGTTTAGTCCGTGCTAAGTCAGGGTTAGCATTAGGTTTGGGTTACTTGGATTTTTATTAATATTAAGGCAGGCTTACATTTGTTATAACTTGGTGAGGATGGTAAAGGGAAGGTTAGTGTATATTTTTGTATATATATAATGTTTTTGTACCCTGTTTCATGCACCATAATAAATCTATAAAAACTCACC
!awk '{print ">"$1"\n"$2}' /Volumes/web/cnidarian/GPL11353_fasta.txt > /Volumes/web/cnidarian/GPL11353_fasta.fa
!tail /Volumes/web/cnidarian/GPL11353_fasta.fa
>AY039650 (sp:O73823) >AJ496218 "(sp:P08906) >AB289857 (sp:P97481) >AJ971237 (sp:Q13231) >AB307634 (sp:Q6L6Q6)
Some are not ESTs
!cat /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_b.fasta \
/Volumes/web/cnidarian/Cgigas_Nuc_NCBI_040414.fasta > \
/Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta \
!fgrep -c ">" /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta
216622
!tail /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta
>gi|2952502|gb|AF051183.1|AF051183 Crassostrea gigas clone BI57x G and T mononucleotide region CTAGACGCCTACCGAATCCACATTCGATAACTGTAGTGGGGGGGGGGGGGNGNGTTGTTTGAAANAAAAA CGTNAAAGGGGCCCTTTTCCTTATNNGNNGAATNCGCCAAANTNAAAANAAAACCGTTTNANTTTAATTT TAAAAAANGGTTAAATTGGTTTAAAACTTTTTTTTTTTTTTTTTTTTTTANCCNGAANCCTTTTTNTNTT CTTTTTTTTNTNTNTNTNTTTTTTTTTTTTTNTNTCTGGGGGGGGGGGGGGGGGGAAAGNATATTTTTTT CCAACCCTGNNAGANTGNGGGAANGTANAAAAGGGTAAANNCCCCCANNNTNNTNTTGGGGGNCCCNNCG CCCTAANGTTAAAGGGGGAANNGTTNGGGNNGNNGGGNCCCCCCCCCGGNCCAGGGGANGGGNANNAAAA A
#tab delimited version
!perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta > /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.tab
Converted 216622 FASTA records in 10632690 lines to tabular format Total sequence length: 706438140
!head /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.tab
gi|318053987|gb|FQ662477.1|FQ662477 FQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence GGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTACAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTTATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAGATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACAATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCCTACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATAAAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGATTAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATTATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTTTATGATCGAAAATGTTTTATTTCCTTTATTATTTATCTGGATATATTATCTGACTCTATACACAAAAGAAGCAAAGCTTTGATGCGTAGTACACATGTGCTGTCAGCCTCATTTTGGTGATGACAATCCAGTTCCTGGTCATCGGTGTGTTTGAAAGCTGCATTCTCCTCAATGTTGTTGGTTTAGCTTCAAGCAAGAGTTTACTTA gi|318053986|gb|FQ662476.1|FQ662476 FQ662476 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF04FM1, mRNA sequence GATCATACATCAAACTGAAGAACATTCATGAAAATCTAACAAGATTGAAAAACACAAAGTTAGAGATTTGTATTAAAACTAAAATATTAGACGAGGTAAAAAAGCTAATTGAATTGCCTTGTCTTGCTGATGTGTCTGCGGATGATATTGTAGATCAAGTTTCTTTAAATATGGAGAATATTGACTATACACGTGCGAAAGGGAATAAAATTTCTGAATTTACAATAGCAGGAACTCGTATAATGGGTGTGAGTTTTTTTGGGTAATGGTAATCTGTTCTTAGCCGACCATAGAGGGAAAAGATGCATCCTTTGTGACACAAATGGAGTTATTTTACAGGAAGCAAAAATACTGGGATCGCCTTGGGGCGTATGTACAAGCGGGATGGATATTCTCATGACGCTTCCAAATGAAAAGTCGATTTTAAAATTTGACTCAACTTCATTTGAAACCATAAAAACTGTTCCTGTTGATTGTTGGTGTTACGGGATAACTGCATCTGGAAACACAATCGTCATTGGTACAGATAGATCTGTTGACATTATAACTGATGGTTTTCTTACTACAAAACGAAAAACACTTTTATCTGGCCTTGGAAATATTAGTGATGTAACAGTAGACAATGAAAATAACGTGATTTGTAGTATTTTTTCTCAACATATTGTCAGAAAACTAGA gi|318053985|gb|FQ662475.1|FQ662475 FQ662475 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF05FM1, mRNA sequence GGAATGCATGCACTTTCAAACAGAAATTATATTTTATGTTTTATTCAACATTTAATTACTGTAATTGCAATTTTCATTTTTCTGAATAATCAAACATTTATAGTGGCCTGATACTGGTGTCATTTATCTCCAGATTATTTATTTCTGAATATACTTTCGAGATCATCTTTTTCTAGAGGTTAGAAGTACTTGATGTAAACAAACTCAAATTACCTGGTTTCAATATTCTAGCTTGAGGATGTGAAATCTAAATGCTTTAGTTTGCAGGCTGCATCATTTGTTCAGTGACTATAGTGAATAGTTTAGAAATTCTTTTTTAGATATGCATGTAGTATTGTATATATTAGTATAAAAAGCATTCATACTTGTTATTTAATTCTGTGATTAAAAAAGAGTTTCTGTGAACAGTATTAGCTTTTATTAATACTGCATTTTTTATTAAAACTACATGCATATTTTTGCTACCTACATGTATTTGTGTTGAATAACGAAATATAACTGTGCAATAAAATCCATGCAAGCATTCAGAATGACAAAACCATATGAAACCAGTGGATATGGAATCAGCAATGGTGTTAACTGATTATTTATTTTCTGAGCTTAATACATCAGCCGATCTTTTCTTTAAAAAAAAATACCAAAACAATAAAATGGACCAATTGTATAGAAAACCAGATACTTTTATTAACATAACATGCGTCTGTTAACAACTTTTTGGGGTGCCATTGGTTGAATATTGTTTGATTATGAATGATGCACTCTATAGTCACGATTATTTATACTATAAAAATAATGC gi|318053984|gb|FQ662474.1|FQ662474 FQ662474 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF06FM1, mRNA sequence GTGAGAGTTCATTGTCGAAAGATGTCTGGTTTTCTTCATCGAGATTCGGTAGTGAATGCAAGTGTAGTAAAGTCGAACATTTTGTTCATGGAAAATGTTTTTCTGATTATTGATACACATAGAGTACATTGATACATGTATATTTGACTTTTTATCTTACACTAAAAGTCAAATCTTGTCAGACGTTTAGTACGTATTTTTAAAAATCCCCAGCTTACATTTGCGTGGAATTCGCTTACTTACAACATACATTTAAAAGCGAGAGTAATACCTAGAAATTTTGTTAACAATAACATGTAAATGATTAGCCTTAAGAAAATCACATATTTGTTTAATATGAATTTCAAATCTAAACAAAACGACCATCAAAATACATGTACATCATGTATGCTTGTAGGGAATTGATTATATCATTATATTTTCACCTAATCAGACTTCGGGCGTCGAAGTAGACGACAACTGCATCCAGTCGTACATTAAACTCCAGCTTCAGCACTCATCTCAATTCATCATCTACCGGCTGTCGGACGACAAAAAACGCATCATTGTCGATAAAATTGGACCAGTTGGGTGTACCTATGACAATTTTGTGCCAGAGCTTCAGAATGCTGGATCTAAGGGAGAGGGTCGGTACGGGGTGTTCGATTTCAATTACACCGTCAAAGAAAGAATAGTAAACAAAATCGTGTTCTTTCTATGGATTCCAGATACAATACAAGTGAAGCAGCGGATGTTATACAGTAGTAGTGTGCGCGCATTANAAACGAGACTTCCCGGAATTCACATAGAAATGCAGTGTAATGACGATTCCG gi|318053983|gb|FQ662473.1|FQ662473 FQ662473 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF07FM1, mRNA sequence GATTCTTGATTTTCTGTATGTTATTCAAATTGGAGGCATCCTTTGTGTGAAATTTGGGATAAATGATTTTGATATATGTAGATCAGTTTCTGTAGTTTGATGACATGTTGAGTGATGTGTAGTATGTGCTGATACATTTCCATTCAGATTTAAATTCTAGCACCCACTACAAGCAATTTCAGGGATAACTTATGAAACATTCCACAAACGTTTTGTGTTACTGATTTTTTTGTGTTCATTTCACGGAAGTTAAATACAAATGAAGAGACTGAATTCACATGAAATGATTCCAATTGTATATATGTCATGTTGTGAATGCTAAACTGTATGTAGTTGGGGAAGGGAGAGGGCATGGAGCCTATTGGATAATTTGTAAATACATTTCTACATTCCATTTTCGTGTACAGAGTGGCGTGTACCTGTATATATGTGTACCTGTATATATGATTACTTACTGTTTTTATACCAATGTTCTGTGAGGAATGATTTTGTCTCGTTTGATGAATTGACAATCCACTCTTTGTTTGGAGAACTTTATCAGATGCACCCCACCGCACGTGTTTCTGCACGGTTTTTGTGAATTTTGAAGACAGTGCAAAATCAACACCCTAGTCTCTTGTCAGATCTGTTATTTTAGTCAAAATATATTTATTTATTAATTTGTTACGATTTTTTGCTATGTTTTTATTGTGTATATTATTTGTACAAGTGTTGAAGTGACAATTTTCTGATCGTTGTTGGGATTACA gi|318053982|gb|FQ662472.1|FQ662472 FQ662472 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF08FM1, mRNA sequence GGAGAACGAGAGATGTAGAGACCATGGATGAAGCGCTAACTCCACTCTAGAACCTTGTGAGATCATCAGTAGAAAGAGACATTCTAATCCGGACCAGAACTTTAGCCACAGCCATTAACCGTAGAATTAGTGTGGAGTTGAATTCTTGTTCCGATTTTAGAAGGTTTTCTTTATTCTGGGTCTTCTTTGTTTCTGTGATTCAAGCCTTTGACTGTTTTTGGAGGAGATAAAAAGGAAACTGTCCTTGAGGATTTTGCCGACGATTGTTCTCAGTAGACACTTACCGCTGTCTTGATCCCTTATGACTTTTTGGAATTTGAATGTTTGACCTAACGAAATGTCTGTGATAAAACGAGATCTATACACATCCAGAAATCCAATCTATACAGCATTATATTTTATTCTGACTGTTCAGTTCTATGGAGTATTAATTTTTGCGGGACATGTAAACGAAAAAGAACAAACATACACATTAAATATACCGTGGCACATAGGAAACCTTCACCCACGACATGTGCAATACACAGTTCACGGAATTCCAGAAATCCAAACCCTCCGACTCAAACGGAACGACAACATTAATATCAACGTGCCCTCCTGTATCATAGATCAGGGTTTTACTATTTGTGAATACGGAAATATACAAGATATTGCCTTCTATCACACTACCGATAAACAAGGGGCGTTTGCAATCACACTGGACCGCACGGCACCAACGGACACACAGACACAACTTGAAGGCGTTTTGGTCTCCGGAAAAGACGCGTTTGTGTTGGAGCCAAATGGTCCCCTGGGACACAGCCTGACCCCCGCCCAC gi|318053981|gb|FQ662471.1|FQ662471 FQ662471 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF09FM1, mRNA sequence GGGAAATGGTGAAAATGGTGGGTGGGCGAGCTGCCAAAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTATCAAGATGGAGGAGATTAAAAAGTTTGCCATAGCTCCAGAAAAGATCCAAGAAGCATTGTATCCTCCCTGTATGAAGGTTTCTGATCTGACTGAGGAAAAGTTGATTACTATAGCTATACGTACAAGATTGTCAGTGCAGGGATATGTGCAATTGGTTAGTAAAATCTATGATGAAGACAGATGTCCAAAAAGAACTCTGATTCTGAAGGAGACAATGGAAGGCAGGCGACCAGCAACCATGTTCGTAAGATTATGGAGGGAGAAGACAGAGATAAATCCTAAAGTGGGATCCTGGTTCAAGTTCTGTCGCTGAAGCTTACTGACTACAAGGACAGCAGAGAAATCCACTCCACCCCCTCCACAGTGCTACGAGAGGTGTCGGAGGAGCAGCCCCCCACACAGACAGACACACAGGCAGCCAGTCAATAAACTCGCACCAAGTACCCGTTAATCTCATTTTCCTCACAGCGGTATAAAGAAGATGTAGACATTTTTTTCCCACTTCATTAATGGTAGCCCTATTTCCACAATTGATTGCTATTGAATTTATAGTAGTCGATCTCTGTAGATTCCTGTCAATGCTTTTGTCTGTCTGTAAGTAGAGGATGCACAGTGCACGTAACCTTAAACCAGTTCTCTAGTTCAAAGGTCAAGATTGAAAGACCTGACAGTAAAACATATACCAATGACTGACTGTGTATCTCTGAAAAAGGTGTGCAATGTACTGTACTTTAACCAA gi|318053980|gb|FQ662470.1|FQ662470 FQ662470 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF10FM1, mRNA sequence GAATCGAGAGGAGATCATCATGTGTATTGTTTTCATTTCCATTTTCACTCTCATCGGTAGAATCATGTAAGAGAAGAGCACGGGTATCTGACAATGTATCTGTTTTAAAATTTTTATAACAATATAATCAATACATTTGATATGTAAGTTAATGCTAGCTGTATTTCTTTCTGTGCTTGGCATGTTGTTCTTAAATACATGAAACATCTACATGTTTTCTTCAATAACTAGCATGAACATATGATAAATATGATAAAAGTGAGTTGGCTGTATGTTTAAAAAATTCCACATCTGTGCGAGTTTTAAAAACTGAAATATTGCTGATTTTTTTTAATGTGATTTCTCATCTTGTAATATAAATATATGGGATGACTGACTTGTAGACCCCTAAAAATGTATATTTTTTAACTTTATTGATTCATAATTGGTAAAATTTTATTCACGAAACTTTTCTACTTGTTAAATTGTATAGAGCTTTTATGTGTACATGTATTACTTTACCTTAATATATTGAGTATTTATATATGCTTAGGTATATACCTAGTCACTGTTATATCTCTGTAGTCCAGAGACTAAGTGTGAAACATACAATGGCTGTGGAGAGTTGTTTTCAAATAATCATAACTGATGCTCATTTTGCTATCTTCTTTCATTGAGTTATCTTTCTTGGTTGTTCATAGTTCTAACGGTTGTGACTATCTTTACATTCCATGCCATGCAATTACATGAATGTGTTCAGAATAAGATTTACAAAATCATTATTAATTTCATATACCAATGTACGTGTATTTTATATGCATTACAACATTTTGAAATCGTTTA gi|318053979|gb|FQ662469.1|FQ662469 FQ662469 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF11FM1, mRNA sequence GATCATATATGGATGATATCTAACATATAGCTGACTTCATTCTTTTTCATTTATTAAATTTGCCCCGTATTACAATCCTTTGGGAGAAGGGGAGACATGTGTTTTTTTGTATAAAAAAACAATACCCACTAGTTTAGAGAGTTCTTGTAGAAAATAATCTGTTGTTGCTACAGATATACCAGATAGTTATTATATTCAGACAGAATGCAACGATTTAGAGTATAACATGTTAAACAATGAAATGCAGTATTCATGTATCAAAATCCAGTAGACAATCTTGAAAACAAGAGCTCATAACTCACCAGACAAAACACAAAGTATTTTTTATGTGCTAGCATTAGAGATACCATATTTTGATATTAAGATTTTTGTGTCATATTTTATGTATGTTCAGTGTGCTTACGGACCAAACAGAGGTTGTGATTGCAAGGTTATTGTAGTGTTATCATAGAGTTGTGAGAGTTATAGAAAGCTAGCTGGTATAGTTTTATACATTCTCTAGAGAACAGTATTTGTTGTTTGTTGTCAATGTTTGAAATACTGTACAAATGTTTGTTAAGTCCATTAACTCTTGCCAAACTAGCAAGTCCCAGCTTACAAAGTGCAATTAGTGGTGTTTTGGTTTGTGTTTTTGTTCCTATCAATCCTGATTCACGGTTTTAAAGAATGTGTGATCATTCATAACAATGTAGAGCTTGCCATGTTTAATGTTCAAATCCAAGGCTTGACTGTTATGCTATGTGTACAATAAATGGGGCCTCAAAA gi|318053978|gb|FQ662468.1|FQ662468 FQ662468 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF12FM1, mRNA sequence GGAAGGGAAACCCCTTCCTTCTGTGGATTTGGGAAAGAAAAATCCTGCCTCCGATTTCAGCAGTTAATGTAAAACGAGAGTGAACTTCAACATTATGGCTGCGGATTTCGAATATAAACAGATGTTATTAGAACTGGATAAGTCTCTGAAAGCCGAAGAATTTGAATCCTTAAAATTTTTATGCAAAGATGAGGTGAAAAAACGAGAAAGAGAAAGTGTCAACCGACCTACAGATTTATGGGAAATTTTGGAGACGAGGGAGAAACTGGGTCCAAATAATCTAGCCTTCTTAAAACAGATAATTAAAGGTTCCTGTAATGGCCGTCGTGATGTTTTGAGAGTTATTGAGAACTTTGAGAGGGGAATTCCACCTGATAGTCAACGACCTGTGAATTCATCATCATCAGTCCCCACGAATCAGCCGTACGTGCAGCAGCCAGTGTTTTATAACCCAGTTCTCAAACAGTATGGGCAACAACCAGGTATGCCTACTCGTGATCATCCCCTGGGTACTTCCATCATCCACTCCAGTGCAGTGAATGTGGACAAATACATGAAAGAAATCAATTTCCTAACGAAGAATTTGGGGAGGGAGTGGAGGTTTTTCATGAGGACCCTTGGAGTGACGGATGGTGATATGATGTCTGTGGAGCAGGACCACCCCCGCAGTTTGAGGGACCAGATTTACCAGTGCCTGGTCCTGTGGATCAGTAACAATGGTGGACAGTTTGACAGGGGCAGAGTAGTTGCGGCACTGCGGGATTCTGCGGTGGAGAGATATGATTTAGCCGGAAGGATTCAAGACTGTG
#Translate pipes to tab so SPID is in separate column for Joining
!tr '|' "\t" </Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.tab> /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab
!head /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab
gi 318053987 gb FQ662477.1 FQ662477 FQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence GGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTACAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTTATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAGATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACAATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCCTACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATAAAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGATTAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATTATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTTTATGATCGAAAATGTTTTATTTCCTTTATTATTTATCTGGATATATTATCTGACTCTATACACAAAAGAAGCAAAGCTTTGATGCGTAGTACACATGTGCTGTCAGCCTCATTTTGGTGATGACAATCCAGTTCCTGGTCATCGGTGTGTTTGAAAGCTGCATTCTCCTCAATGTTGTTGGTTTAGCTTCAAGCAAGAGTTTACTTA gi 318053986 gb FQ662476.1 FQ662476 FQ662476 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF04FM1, mRNA sequence GATCATACATCAAACTGAAGAACATTCATGAAAATCTAACAAGATTGAAAAACACAAAGTTAGAGATTTGTATTAAAACTAAAATATTAGACGAGGTAAAAAAGCTAATTGAATTGCCTTGTCTTGCTGATGTGTCTGCGGATGATATTGTAGATCAAGTTTCTTTAAATATGGAGAATATTGACTATACACGTGCGAAAGGGAATAAAATTTCTGAATTTACAATAGCAGGAACTCGTATAATGGGTGTGAGTTTTTTTGGGTAATGGTAATCTGTTCTTAGCCGACCATAGAGGGAAAAGATGCATCCTTTGTGACACAAATGGAGTTATTTTACAGGAAGCAAAAATACTGGGATCGCCTTGGGGCGTATGTACAAGCGGGATGGATATTCTCATGACGCTTCCAAATGAAAAGTCGATTTTAAAATTTGACTCAACTTCATTTGAAACCATAAAAACTGTTCCTGTTGATTGTTGGTGTTACGGGATAACTGCATCTGGAAACACAATCGTCATTGGTACAGATAGATCTGTTGACATTATAACTGATGGTTTTCTTACTACAAAACGAAAAACACTTTTATCTGGCCTTGGAAATATTAGTGATGTAACAGTAGACAATGAAAATAACGTGATTTGTAGTATTTTTTCTCAACATATTGTCAGAAAACTAGA gi 318053985 gb FQ662475.1 FQ662475 FQ662475 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF05FM1, mRNA sequence GGAATGCATGCACTTTCAAACAGAAATTATATTTTATGTTTTATTCAACATTTAATTACTGTAATTGCAATTTTCATTTTTCTGAATAATCAAACATTTATAGTGGCCTGATACTGGTGTCATTTATCTCCAGATTATTTATTTCTGAATATACTTTCGAGATCATCTTTTTCTAGAGGTTAGAAGTACTTGATGTAAACAAACTCAAATTACCTGGTTTCAATATTCTAGCTTGAGGATGTGAAATCTAAATGCTTTAGTTTGCAGGCTGCATCATTTGTTCAGTGACTATAGTGAATAGTTTAGAAATTCTTTTTTAGATATGCATGTAGTATTGTATATATTAGTATAAAAAGCATTCATACTTGTTATTTAATTCTGTGATTAAAAAAGAGTTTCTGTGAACAGTATTAGCTTTTATTAATACTGCATTTTTTATTAAAACTACATGCATATTTTTGCTACCTACATGTATTTGTGTTGAATAACGAAATATAACTGTGCAATAAAATCCATGCAAGCATTCAGAATGACAAAACCATATGAAACCAGTGGATATGGAATCAGCAATGGTGTTAACTGATTATTTATTTTCTGAGCTTAATACATCAGCCGATCTTTTCTTTAAAAAAAAATACCAAAACAATAAAATGGACCAATTGTATAGAAAACCAGATACTTTTATTAACATAACATGCGTCTGTTAACAACTTTTTGGGGTGCCATTGGTTGAATATTGTTTGATTATGAATGATGCACTCTATAGTCACGATTATTTATACTATAAAAATAATGC gi 318053984 gb FQ662474.1 FQ662474 FQ662474 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF06FM1, mRNA sequence GTGAGAGTTCATTGTCGAAAGATGTCTGGTTTTCTTCATCGAGATTCGGTAGTGAATGCAAGTGTAGTAAAGTCGAACATTTTGTTCATGGAAAATGTTTTTCTGATTATTGATACACATAGAGTACATTGATACATGTATATTTGACTTTTTATCTTACACTAAAAGTCAAATCTTGTCAGACGTTTAGTACGTATTTTTAAAAATCCCCAGCTTACATTTGCGTGGAATTCGCTTACTTACAACATACATTTAAAAGCGAGAGTAATACCTAGAAATTTTGTTAACAATAACATGTAAATGATTAGCCTTAAGAAAATCACATATTTGTTTAATATGAATTTCAAATCTAAACAAAACGACCATCAAAATACATGTACATCATGTATGCTTGTAGGGAATTGATTATATCATTATATTTTCACCTAATCAGACTTCGGGCGTCGAAGTAGACGACAACTGCATCCAGTCGTACATTAAACTCCAGCTTCAGCACTCATCTCAATTCATCATCTACCGGCTGTCGGACGACAAAAAACGCATCATTGTCGATAAAATTGGACCAGTTGGGTGTACCTATGACAATTTTGTGCCAGAGCTTCAGAATGCTGGATCTAAGGGAGAGGGTCGGTACGGGGTGTTCGATTTCAATTACACCGTCAAAGAAAGAATAGTAAACAAAATCGTGTTCTTTCTATGGATTCCAGATACAATACAAGTGAAGCAGCGGATGTTATACAGTAGTAGTGTGCGCGCATTANAAACGAGACTTCCCGGAATTCACATAGAAATGCAGTGTAATGACGATTCCG gi 318053983 gb FQ662473.1 FQ662473 FQ662473 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF07FM1, mRNA sequence GATTCTTGATTTTCTGTATGTTATTCAAATTGGAGGCATCCTTTGTGTGAAATTTGGGATAAATGATTTTGATATATGTAGATCAGTTTCTGTAGTTTGATGACATGTTGAGTGATGTGTAGTATGTGCTGATACATTTCCATTCAGATTTAAATTCTAGCACCCACTACAAGCAATTTCAGGGATAACTTATGAAACATTCCACAAACGTTTTGTGTTACTGATTTTTTTGTGTTCATTTCACGGAAGTTAAATACAAATGAAGAGACTGAATTCACATGAAATGATTCCAATTGTATATATGTCATGTTGTGAATGCTAAACTGTATGTAGTTGGGGAAGGGAGAGGGCATGGAGCCTATTGGATAATTTGTAAATACATTTCTACATTCCATTTTCGTGTACAGAGTGGCGTGTACCTGTATATATGTGTACCTGTATATATGATTACTTACTGTTTTTATACCAATGTTCTGTGAGGAATGATTTTGTCTCGTTTGATGAATTGACAATCCACTCTTTGTTTGGAGAACTTTATCAGATGCACCCCACCGCACGTGTTTCTGCACGGTTTTTGTGAATTTTGAAGACAGTGCAAAATCAACACCCTAGTCTCTTGTCAGATCTGTTATTTTAGTCAAAATATATTTATTTATTAATTTGTTACGATTTTTTGCTATGTTTTTATTGTGTATATTATTTGTACAAGTGTTGAAGTGACAATTTTCTGATCGTTGTTGGGATTACA gi 318053982 gb FQ662472.1 FQ662472 FQ662472 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF08FM1, mRNA sequence GGAGAACGAGAGATGTAGAGACCATGGATGAAGCGCTAACTCCACTCTAGAACCTTGTGAGATCATCAGTAGAAAGAGACATTCTAATCCGGACCAGAACTTTAGCCACAGCCATTAACCGTAGAATTAGTGTGGAGTTGAATTCTTGTTCCGATTTTAGAAGGTTTTCTTTATTCTGGGTCTTCTTTGTTTCTGTGATTCAAGCCTTTGACTGTTTTTGGAGGAGATAAAAAGGAAACTGTCCTTGAGGATTTTGCCGACGATTGTTCTCAGTAGACACTTACCGCTGTCTTGATCCCTTATGACTTTTTGGAATTTGAATGTTTGACCTAACGAAATGTCTGTGATAAAACGAGATCTATACACATCCAGAAATCCAATCTATACAGCATTATATTTTATTCTGACTGTTCAGTTCTATGGAGTATTAATTTTTGCGGGACATGTAAACGAAAAAGAACAAACATACACATTAAATATACCGTGGCACATAGGAAACCTTCACCCACGACATGTGCAATACACAGTTCACGGAATTCCAGAAATCCAAACCCTCCGACTCAAACGGAACGACAACATTAATATCAACGTGCCCTCCTGTATCATAGATCAGGGTTTTACTATTTGTGAATACGGAAATATACAAGATATTGCCTTCTATCACACTACCGATAAACAAGGGGCGTTTGCAATCACACTGGACCGCACGGCACCAACGGACACACAGACACAACTTGAAGGCGTTTTGGTCTCCGGAAAAGACGCGTTTGTGTTGGAGCCAAATGGTCCCCTGGGACACAGCCTGACCCCCGCCCAC gi 318053981 gb FQ662471.1 FQ662471 FQ662471 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF09FM1, mRNA sequence GGGAAATGGTGAAAATGGTGGGTGGGCGAGCTGCCAAAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTATCAAGATGGAGGAGATTAAAAAGTTTGCCATAGCTCCAGAAAAGATCCAAGAAGCATTGTATCCTCCCTGTATGAAGGTTTCTGATCTGACTGAGGAAAAGTTGATTACTATAGCTATACGTACAAGATTGTCAGTGCAGGGATATGTGCAATTGGTTAGTAAAATCTATGATGAAGACAGATGTCCAAAAAGAACTCTGATTCTGAAGGAGACAATGGAAGGCAGGCGACCAGCAACCATGTTCGTAAGATTATGGAGGGAGAAGACAGAGATAAATCCTAAAGTGGGATCCTGGTTCAAGTTCTGTCGCTGAAGCTTACTGACTACAAGGACAGCAGAGAAATCCACTCCACCCCCTCCACAGTGCTACGAGAGGTGTCGGAGGAGCAGCCCCCCACACAGACAGACACACAGGCAGCCAGTCAATAAACTCGCACCAAGTACCCGTTAATCTCATTTTCCTCACAGCGGTATAAAGAAGATGTAGACATTTTTTTCCCACTTCATTAATGGTAGCCCTATTTCCACAATTGATTGCTATTGAATTTATAGTAGTCGATCTCTGTAGATTCCTGTCAATGCTTTTGTCTGTCTGTAAGTAGAGGATGCACAGTGCACGTAACCTTAAACCAGTTCTCTAGTTCAAAGGTCAAGATTGAAAGACCTGACAGTAAAACATATACCAATGACTGACTGTGTATCTCTGAAAAAGGTGTGCAATGTACTGTACTTTAACCAA gi 318053980 gb FQ662470.1 FQ662470 FQ662470 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF10FM1, mRNA sequence GAATCGAGAGGAGATCATCATGTGTATTGTTTTCATTTCCATTTTCACTCTCATCGGTAGAATCATGTAAGAGAAGAGCACGGGTATCTGACAATGTATCTGTTTTAAAATTTTTATAACAATATAATCAATACATTTGATATGTAAGTTAATGCTAGCTGTATTTCTTTCTGTGCTTGGCATGTTGTTCTTAAATACATGAAACATCTACATGTTTTCTTCAATAACTAGCATGAACATATGATAAATATGATAAAAGTGAGTTGGCTGTATGTTTAAAAAATTCCACATCTGTGCGAGTTTTAAAAACTGAAATATTGCTGATTTTTTTTAATGTGATTTCTCATCTTGTAATATAAATATATGGGATGACTGACTTGTAGACCCCTAAAAATGTATATTTTTTAACTTTATTGATTCATAATTGGTAAAATTTTATTCACGAAACTTTTCTACTTGTTAAATTGTATAGAGCTTTTATGTGTACATGTATTACTTTACCTTAATATATTGAGTATTTATATATGCTTAGGTATATACCTAGTCACTGTTATATCTCTGTAGTCCAGAGACTAAGTGTGAAACATACAATGGCTGTGGAGAGTTGTTTTCAAATAATCATAACTGATGCTCATTTTGCTATCTTCTTTCATTGAGTTATCTTTCTTGGTTGTTCATAGTTCTAACGGTTGTGACTATCTTTACATTCCATGCCATGCAATTACATGAATGTGTTCAGAATAAGATTTACAAAATCATTATTAATTTCATATACCAATGTACGTGTATTTTATATGCATTACAACATTTTGAAATCGTTTA gi 318053979 gb FQ662469.1 FQ662469 FQ662469 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF11FM1, mRNA sequence GATCATATATGGATGATATCTAACATATAGCTGACTTCATTCTTTTTCATTTATTAAATTTGCCCCGTATTACAATCCTTTGGGAGAAGGGGAGACATGTGTTTTTTTGTATAAAAAAACAATACCCACTAGTTTAGAGAGTTCTTGTAGAAAATAATCTGTTGTTGCTACAGATATACCAGATAGTTATTATATTCAGACAGAATGCAACGATTTAGAGTATAACATGTTAAACAATGAAATGCAGTATTCATGTATCAAAATCCAGTAGACAATCTTGAAAACAAGAGCTCATAACTCACCAGACAAAACACAAAGTATTTTTTATGTGCTAGCATTAGAGATACCATATTTTGATATTAAGATTTTTGTGTCATATTTTATGTATGTTCAGTGTGCTTACGGACCAAACAGAGGTTGTGATTGCAAGGTTATTGTAGTGTTATCATAGAGTTGTGAGAGTTATAGAAAGCTAGCTGGTATAGTTTTATACATTCTCTAGAGAACAGTATTTGTTGTTTGTTGTCAATGTTTGAAATACTGTACAAATGTTTGTTAAGTCCATTAACTCTTGCCAAACTAGCAAGTCCCAGCTTACAAAGTGCAATTAGTGGTGTTTTGGTTTGTGTTTTTGTTCCTATCAATCCTGATTCACGGTTTTAAAGAATGTGTGATCATTCATAACAATGTAGAGCTTGCCATGTTTAATGTTCAAATCCAAGGCTTGACTGTTATGCTATGTGTACAATAAATGGGGCCTCAAAA gi 318053978 gb FQ662468.1 FQ662468 FQ662468 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF12FM1, mRNA sequence GGAAGGGAAACCCCTTCCTTCTGTGGATTTGGGAAAGAAAAATCCTGCCTCCGATTTCAGCAGTTAATGTAAAACGAGAGTGAACTTCAACATTATGGCTGCGGATTTCGAATATAAACAGATGTTATTAGAACTGGATAAGTCTCTGAAAGCCGAAGAATTTGAATCCTTAAAATTTTTATGCAAAGATGAGGTGAAAAAACGAGAAAGAGAAAGTGTCAACCGACCTACAGATTTATGGGAAATTTTGGAGACGAGGGAGAAACTGGGTCCAAATAATCTAGCCTTCTTAAAACAGATAATTAAAGGTTCCTGTAATGGCCGTCGTGATGTTTTGAGAGTTATTGAGAACTTTGAGAGGGGAATTCCACCTGATAGTCAACGACCTGTGAATTCATCATCATCAGTCCCCACGAATCAGCCGTACGTGCAGCAGCCAGTGTTTTATAACCCAGTTCTCAAACAGTATGGGCAACAACCAGGTATGCCTACTCGTGATCATCCCCTGGGTACTTCCATCATCCACTCCAGTGCAGTGAATGTGGACAAATACATGAAAGAAATCAATTTCCTAACGAAGAATTTGGGGAGGGAGTGGAGGTTTTTCATGAGGACCCTTGGAGTGACGGATGGTGATATGATGTCTGTGGAGCAGGACCACCCCCGCAGTTTGAGGGACCAGATTTACCAGTGCCTGGTCCTGTGGATCAGTAACAATGGTGGACAGTTTGACAGGGGCAGAGTAGTTGCGGCACTGCGGGATTCTGCGGTGGAGAGATATGATTTAGCCGGAAGGATTCAAGACTGTG
!head /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab
gi 318053987 gb FQ662477.1 FQ662477 FQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence GGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTACAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTTATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAGATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACAATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCCTACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATAAAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGATTAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATTATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTTTATGATCGAAAATGTTTTATTTCCTTTATTATTTATCTGGATATATTATCTGACTCTATACACAAAAGAAGCAAAGCTTTGATGCGTAGTACACATGTGCTGTCAGCCTCATTTTGGTGATGACAATCCAGTTCCTGGTCATCGGTGTGTTTGAAAGCTGCATTCTCCTCAATGTTGTTGGTTTAGCTTCAAGCAAGAGTTTACTTA gi 318053986 gb FQ662476.1 FQ662476 FQ662476 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF04FM1, mRNA sequence GATCATACATCAAACTGAAGAACATTCATGAAAATCTAACAAGATTGAAAAACACAAAGTTAGAGATTTGTATTAAAACTAAAATATTAGACGAGGTAAAAAAGCTAATTGAATTGCCTTGTCTTGCTGATGTGTCTGCGGATGATATTGTAGATCAAGTTTCTTTAAATATGGAGAATATTGACTATACACGTGCGAAAGGGAATAAAATTTCTGAATTTACAATAGCAGGAACTCGTATAATGGGTGTGAGTTTTTTTGGGTAATGGTAATCTGTTCTTAGCCGACCATAGAGGGAAAAGATGCATCCTTTGTGACACAAATGGAGTTATTTTACAGGAAGCAAAAATACTGGGATCGCCTTGGGGCGTATGTACAAGCGGGATGGATATTCTCATGACGCTTCCAAATGAAAAGTCGATTTTAAAATTTGACTCAACTTCATTTGAAACCATAAAAACTGTTCCTGTTGATTGTTGGTGTTACGGGATAACTGCATCTGGAAACACAATCGTCATTGGTACAGATAGATCTGTTGACATTATAACTGATGGTTTTCTTACTACAAAACGAAAAACACTTTTATCTGGCCTTGGAAATATTAGTGATGTAACAGTAGACAATGAAAATAACGTGATTTGTAGTATTTTTTCTCAACATATTGTCAGAAAACTAGA gi 318053985 gb FQ662475.1 FQ662475 FQ662475 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF05FM1, mRNA sequence GGAATGCATGCACTTTCAAACAGAAATTATATTTTATGTTTTATTCAACATTTAATTACTGTAATTGCAATTTTCATTTTTCTGAATAATCAAACATTTATAGTGGCCTGATACTGGTGTCATTTATCTCCAGATTATTTATTTCTGAATATACTTTCGAGATCATCTTTTTCTAGAGGTTAGAAGTACTTGATGTAAACAAACTCAAATTACCTGGTTTCAATATTCTAGCTTGAGGATGTGAAATCTAAATGCTTTAGTTTGCAGGCTGCATCATTTGTTCAGTGACTATAGTGAATAGTTTAGAAATTCTTTTTTAGATATGCATGTAGTATTGTATATATTAGTATAAAAAGCATTCATACTTGTTATTTAATTCTGTGATTAAAAAAGAGTTTCTGTGAACAGTATTAGCTTTTATTAATACTGCATTTTTTATTAAAACTACATGCATATTTTTGCTACCTACATGTATTTGTGTTGAATAACGAAATATAACTGTGCAATAAAATCCATGCAAGCATTCAGAATGACAAAACCATATGAAACCAGTGGATATGGAATCAGCAATGGTGTTAACTGATTATTTATTTTCTGAGCTTAATACATCAGCCGATCTTTTCTTTAAAAAAAAATACCAAAACAATAAAATGGACCAATTGTATAGAAAACCAGATACTTTTATTAACATAACATGCGTCTGTTAACAACTTTTTGGGGTGCCATTGGTTGAATATTGTTTGATTATGAATGATGCACTCTATAGTCACGATTATTTATACTATAAAAATAATGC gi 318053984 gb FQ662474.1 FQ662474 FQ662474 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF06FM1, mRNA sequence GTGAGAGTTCATTGTCGAAAGATGTCTGGTTTTCTTCATCGAGATTCGGTAGTGAATGCAAGTGTAGTAAAGTCGAACATTTTGTTCATGGAAAATGTTTTTCTGATTATTGATACACATAGAGTACATTGATACATGTATATTTGACTTTTTATCTTACACTAAAAGTCAAATCTTGTCAGACGTTTAGTACGTATTTTTAAAAATCCCCAGCTTACATTTGCGTGGAATTCGCTTACTTACAACATACATTTAAAAGCGAGAGTAATACCTAGAAATTTTGTTAACAATAACATGTAAATGATTAGCCTTAAGAAAATCACATATTTGTTTAATATGAATTTCAAATCTAAACAAAACGACCATCAAAATACATGTACATCATGTATGCTTGTAGGGAATTGATTATATCATTATATTTTCACCTAATCAGACTTCGGGCGTCGAAGTAGACGACAACTGCATCCAGTCGTACATTAAACTCCAGCTTCAGCACTCATCTCAATTCATCATCTACCGGCTGTCGGACGACAAAAAACGCATCATTGTCGATAAAATTGGACCAGTTGGGTGTACCTATGACAATTTTGTGCCAGAGCTTCAGAATGCTGGATCTAAGGGAGAGGGTCGGTACGGGGTGTTCGATTTCAATTACACCGTCAAAGAAAGAATAGTAAACAAAATCGTGTTCTTTCTATGGATTCCAGATACAATACAAGTGAAGCAGCGGATGTTATACAGTAGTAGTGTGCGCGCATTANAAACGAGACTTCCCGGAATTCACATAGAAATGCAGTGTAATGACGATTCCG gi 318053983 gb FQ662473.1 FQ662473 FQ662473 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF07FM1, mRNA sequence GATTCTTGATTTTCTGTATGTTATTCAAATTGGAGGCATCCTTTGTGTGAAATTTGGGATAAATGATTTTGATATATGTAGATCAGTTTCTGTAGTTTGATGACATGTTGAGTGATGTGTAGTATGTGCTGATACATTTCCATTCAGATTTAAATTCTAGCACCCACTACAAGCAATTTCAGGGATAACTTATGAAACATTCCACAAACGTTTTGTGTTACTGATTTTTTTGTGTTCATTTCACGGAAGTTAAATACAAATGAAGAGACTGAATTCACATGAAATGATTCCAATTGTATATATGTCATGTTGTGAATGCTAAACTGTATGTAGTTGGGGAAGGGAGAGGGCATGGAGCCTATTGGATAATTTGTAAATACATTTCTACATTCCATTTTCGTGTACAGAGTGGCGTGTACCTGTATATATGTGTACCTGTATATATGATTACTTACTGTTTTTATACCAATGTTCTGTGAGGAATGATTTTGTCTCGTTTGATGAATTGACAATCCACTCTTTGTTTGGAGAACTTTATCAGATGCACCCCACCGCACGTGTTTCTGCACGGTTTTTGTGAATTTTGAAGACAGTGCAAAATCAACACCCTAGTCTCTTGTCAGATCTGTTATTTTAGTCAAAATATATTTATTTATTAATTTGTTACGATTTTTTGCTATGTTTTTATTGTGTATATTATTTGTACAAGTGTTGAAGTGACAATTTTCTGATCGTTGTTGGGATTACA gi 318053982 gb FQ662472.1 FQ662472 FQ662472 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF08FM1, mRNA sequence GGAGAACGAGAGATGTAGAGACCATGGATGAAGCGCTAACTCCACTCTAGAACCTTGTGAGATCATCAGTAGAAAGAGACATTCTAATCCGGACCAGAACTTTAGCCACAGCCATTAACCGTAGAATTAGTGTGGAGTTGAATTCTTGTTCCGATTTTAGAAGGTTTTCTTTATTCTGGGTCTTCTTTGTTTCTGTGATTCAAGCCTTTGACTGTTTTTGGAGGAGATAAAAAGGAAACTGTCCTTGAGGATTTTGCCGACGATTGTTCTCAGTAGACACTTACCGCTGTCTTGATCCCTTATGACTTTTTGGAATTTGAATGTTTGACCTAACGAAATGTCTGTGATAAAACGAGATCTATACACATCCAGAAATCCAATCTATACAGCATTATATTTTATTCTGACTGTTCAGTTCTATGGAGTATTAATTTTTGCGGGACATGTAAACGAAAAAGAACAAACATACACATTAAATATACCGTGGCACATAGGAAACCTTCACCCACGACATGTGCAATACACAGTTCACGGAATTCCAGAAATCCAAACCCTCCGACTCAAACGGAACGACAACATTAATATCAACGTGCCCTCCTGTATCATAGATCAGGGTTTTACTATTTGTGAATACGGAAATATACAAGATATTGCCTTCTATCACACTACCGATAAACAAGGGGCGTTTGCAATCACACTGGACCGCACGGCACCAACGGACACACAGACACAACTTGAAGGCGTTTTGGTCTCCGGAAAAGACGCGTTTGTGTTGGAGCCAAATGGTCCCCTGGGACACAGCCTGACCCCCGCCCAC gi 318053981 gb FQ662471.1 FQ662471 FQ662471 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF09FM1, mRNA sequence GGGAAATGGTGAAAATGGTGGGTGGGCGAGCTGCCAAAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTATCAAGATGGAGGAGATTAAAAAGTTTGCCATAGCTCCAGAAAAGATCCAAGAAGCATTGTATCCTCCCTGTATGAAGGTTTCTGATCTGACTGAGGAAAAGTTGATTACTATAGCTATACGTACAAGATTGTCAGTGCAGGGATATGTGCAATTGGTTAGTAAAATCTATGATGAAGACAGATGTCCAAAAAGAACTCTGATTCTGAAGGAGACAATGGAAGGCAGGCGACCAGCAACCATGTTCGTAAGATTATGGAGGGAGAAGACAGAGATAAATCCTAAAGTGGGATCCTGGTTCAAGTTCTGTCGCTGAAGCTTACTGACTACAAGGACAGCAGAGAAATCCACTCCACCCCCTCCACAGTGCTACGAGAGGTGTCGGAGGAGCAGCCCCCCACACAGACAGACACACAGGCAGCCAGTCAATAAACTCGCACCAAGTACCCGTTAATCTCATTTTCCTCACAGCGGTATAAAGAAGATGTAGACATTTTTTTCCCACTTCATTAATGGTAGCCCTATTTCCACAATTGATTGCTATTGAATTTATAGTAGTCGATCTCTGTAGATTCCTGTCAATGCTTTTGTCTGTCTGTAAGTAGAGGATGCACAGTGCACGTAACCTTAAACCAGTTCTCTAGTTCAAAGGTCAAGATTGAAAGACCTGACAGTAAAACATATACCAATGACTGACTGTGTATCTCTGAAAAAGGTGTGCAATGTACTGTACTTTAACCAA gi 318053980 gb FQ662470.1 FQ662470 FQ662470 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF10FM1, mRNA sequence GAATCGAGAGGAGATCATCATGTGTATTGTTTTCATTTCCATTTTCACTCTCATCGGTAGAATCATGTAAGAGAAGAGCACGGGTATCTGACAATGTATCTGTTTTAAAATTTTTATAACAATATAATCAATACATTTGATATGTAAGTTAATGCTAGCTGTATTTCTTTCTGTGCTTGGCATGTTGTTCTTAAATACATGAAACATCTACATGTTTTCTTCAATAACTAGCATGAACATATGATAAATATGATAAAAGTGAGTTGGCTGTATGTTTAAAAAATTCCACATCTGTGCGAGTTTTAAAAACTGAAATATTGCTGATTTTTTTTAATGTGATTTCTCATCTTGTAATATAAATATATGGGATGACTGACTTGTAGACCCCTAAAAATGTATATTTTTTAACTTTATTGATTCATAATTGGTAAAATTTTATTCACGAAACTTTTCTACTTGTTAAATTGTATAGAGCTTTTATGTGTACATGTATTACTTTACCTTAATATATTGAGTATTTATATATGCTTAGGTATATACCTAGTCACTGTTATATCTCTGTAGTCCAGAGACTAAGTGTGAAACATACAATGGCTGTGGAGAGTTGTTTTCAAATAATCATAACTGATGCTCATTTTGCTATCTTCTTTCATTGAGTTATCTTTCTTGGTTGTTCATAGTTCTAACGGTTGTGACTATCTTTACATTCCATGCCATGCAATTACATGAATGTGTTCAGAATAAGATTTACAAAATCATTATTAATTTCATATACCAATGTACGTGTATTTTATATGCATTACAACATTTTGAAATCGTTTA gi 318053979 gb FQ662469.1 FQ662469 FQ662469 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF11FM1, mRNA sequence GATCATATATGGATGATATCTAACATATAGCTGACTTCATTCTTTTTCATTTATTAAATTTGCCCCGTATTACAATCCTTTGGGAGAAGGGGAGACATGTGTTTTTTTGTATAAAAAAACAATACCCACTAGTTTAGAGAGTTCTTGTAGAAAATAATCTGTTGTTGCTACAGATATACCAGATAGTTATTATATTCAGACAGAATGCAACGATTTAGAGTATAACATGTTAAACAATGAAATGCAGTATTCATGTATCAAAATCCAGTAGACAATCTTGAAAACAAGAGCTCATAACTCACCAGACAAAACACAAAGTATTTTTTATGTGCTAGCATTAGAGATACCATATTTTGATATTAAGATTTTTGTGTCATATTTTATGTATGTTCAGTGTGCTTACGGACCAAACAGAGGTTGTGATTGCAAGGTTATTGTAGTGTTATCATAGAGTTGTGAGAGTTATAGAAAGCTAGCTGGTATAGTTTTATACATTCTCTAGAGAACAGTATTTGTTGTTTGTTGTCAATGTTTGAAATACTGTACAAATGTTTGTTAAGTCCATTAACTCTTGCCAAACTAGCAAGTCCCAGCTTACAAAGTGCAATTAGTGGTGTTTTGGTTTGTGTTTTTGTTCCTATCAATCCTGATTCACGGTTTTAAAGAATGTGTGATCATTCATAACAATGTAGAGCTTGCCATGTTTAATGTTCAAATCCAAGGCTTGACTGTTATGCTATGTGTACAATAAATGGGGCCTCAAAA gi 318053978 gb FQ662468.1 FQ662468 FQ662468 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF12FM1, mRNA sequence GGAAGGGAAACCCCTTCCTTCTGTGGATTTGGGAAAGAAAAATCCTGCCTCCGATTTCAGCAGTTAATGTAAAACGAGAGTGAACTTCAACATTATGGCTGCGGATTTCGAATATAAACAGATGTTATTAGAACTGGATAAGTCTCTGAAAGCCGAAGAATTTGAATCCTTAAAATTTTTATGCAAAGATGAGGTGAAAAAACGAGAAAGAGAAAGTGTCAACCGACCTACAGATTTATGGGAAATTTTGGAGACGAGGGAGAAACTGGGTCCAAATAATCTAGCCTTCTTAAAACAGATAATTAAAGGTTCCTGTAATGGCCGTCGTGATGTTTTGAGAGTTATTGAGAACTTTGAGAGGGGAATTCCACCTGATAGTCAACGACCTGTGAATTCATCATCATCAGTCCCCACGAATCAGCCGTACGTGCAGCAGCCAGTGTTTTATAACCCAGTTCTCAAACAGTATGGGCAACAACCAGGTATGCCTACTCGTGATCATCCCCTGGGTACTTCCATCATCCACTCCAGTGCAGTGAATGTGGACAAATACATGAAAGAAATCAATTTCCTAACGAAGAATTTGGGGAGGGAGTGGAGGTTTTTCATGAGGACCCTTGGAGTGACGGATGGTGATATGATGTCTGTGGAGCAGGACCACCCCCGCAGTTTGAGGGACCAGATTTACCAGTGCCTGGTCCTGTGGATCAGTAACAATGGTGGACAGTTTGACAGGGGCAGAGTAGTTGCGGCACTGCGGGATTCTGCGGTGGAGAGATATGATTTAGCCGGAAGGATTCAAGACTGTG
!awk '{print $5,$NF}' /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab > /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab
!tail /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab
AF280611 CGCCTGTTTATCAAAAACATCACTAGAAGATAAAGACTTTTAGCAATACCCGCCCAGTGCGAAATATTACTGTAAACGGCCGCCCTAGCGTGAGGGTGCTAAGGTAGCGAAATTCCTTGCCTTTTGATTGTGGGCCTGCATGAATGGTTTAACGAGGGTTTGACTGTCTCTAAATTTTTTATTGAAATTGTACTGAAGGTGAAGATACCTTCATTTAAAAGTTAGACAAAAAGACCCCGTGCAACTTTGAAAATTAACTTTATTCAGGAGTAAAAGATTTTTAGGTGGGGCGCCTAGAAAGCAAGTCTAACCTTTCTGAATAACTAACTCTTTCCGGATTTGACCCGATTATATTCGATCATAGGAGAAGTTACGCCGGGGATAACAGGCTAATCCTTTAGTAGAGTTCGTATTGGCTAAAGGGATTGGCACCTCGATGTTGAATCAGGGATAATAGCTTCAAGGCGTAGAGGCTTTGAAAGTAGGTCTGTTCGACCTTTAATACCCTACGTGATCTGAGTTCAGACCGG Crassostrea TGTAATACGCCTGAGTTGGAGACAATTTTTAAGGTAGCGCGAGTAGAAAGTTTTAAAATTTGCTTACTGCTAGGTTTGCTTCAATTTTGATATTTTTAATAACCTATTTGTAAGCCTCTATTACATGACGTAAATTTTTAGAATTGTCTTAAAGTTTAATTACATGTAGCTTATGTGTTAACCGTTATCTTTGTGAAGTGAAATACAGCTTAAGTAAAAAAAATAAAATATCTTTTCCCTATGTAATAAAAGGAGTTTTAGTGTCTTAACCTATAGCGATTCGTGCTTAGTCTAAGCTGATAGTGGCAGCCAAATTAAAATTTGGTGTTGAATGAATTGCTTGCAAGCAGGTTAAAAAATCAACTTGGTCTATTAGGGTGGTAAAGTAAAAGTATTGGGTGAAGCCTTATAAAATATTGAAAAGTACTATAAGTTAATTCTAATAAGCATACAGGGAGTGCAATAGGTTGGGTATAATAATAAATGTTTAAGTAATAAAAAATGATGAGTAGCAATAAATTGTTTGGGTATAAAAGTGATTAGCTTGGGTTAGAAGAAATCATAAAGGCTTGGGTGTAAGTTTTAAAAATAAATATGATAAGATCGAAGGTTAAGTTGAGTGCGCTTTATAAGGCACATTAGTGT Crassostrea CTTATCCCTTTGATGCTTCTAGTAGCAGACATGCAATTTCCTCGATTAAATGCATTTAGATTTTGAGTTTTGCCAGGGTCTCTTTATCTTATGCTTATGTCTAACATTGTAGAAAACGGAGTTGGGGCAGGGTGAACAATTTACCCTCCTTTATCAACTTACTCTTATCATGGAGTTTGTATAGACCTTGCAATTCTAAGCCTTCACCTTGCTGGTATTAGCTCTATTTTCAGGTCAATTAATTTCATAGTAACGATTAGAAATATGCGATCTGTTGGGGGCCATTTACTAGCACTATTCCCTTGATCTATTAAGGTTACTTCATTCTTGCTTTTGACTACTCTCCCAGTGTTAGCTGGAGGTCTTACTATACTTTTGACTGATCGTCATTTTAATACCTCTTTTTTTGACCCTGTCGGAGGGGGGGACCCTGTCTTATTTCAGCATTTGTTTTGATTTTTTGGTCACCCTGAGGTGTATGTCCTTATTCTTCCAGGTTTTGGAATAATTTCTCATGTCTTATGTTTTTGGTCAAGTAAAAAGACTGCATATGGAAATATGGGAATGTTTTATGCAATACTTAATATTGGGTTCTTAGGGTTTATTGTCTGGGGGCATCACATGTTTGTGGCTGGAATGGATATTGATACGCGTGCTTATTTTAGTGCTGCCACCGTTATTATTGCAGTGCCAACTGGTATTAAGGTGTTTGCATGAATTAGCACAATGCTAGGCTCTAAAGTTTCAACTCAAGCACCTATGTTGTGGTCTACTGGTTTTATTATTCTTTTTACAACAGGGGGTCTTACAGGACTTATTCTATCAAGAGCTTCAGTAGATGTGACGCTTCACGACACTTATTTTGTAACTGGTCATTTTCACTACGTCTTATCA AF288678 TGTAAAACGAGTCAGTCGAGTGAAAAAATTAAACGTTTCTCATATTTCAGCCAGATATAAATTGTTAACTGGATCCAGGCATTTTTCAACATCAAAACAATGGAATAAAGCACTAGTGTTAGGCGTGTATGAGAATGAATCTACAGACTCCATTGATTTTACTGGAACAGCAAGAAAATTTGATGAAAAAGCAGATGGAAAAATTTCACAGCTGTTGCTAACAGTAAAGAAGCCACTAAAATGTGGAAAAACAAGAACACTACATGCAGTAGTCCCAGAGTTTTCTTCAGTGTTAGTGACCTGCATTGGAAAAAGAGGAGAGGGATATGATGAACTGGAGACAGTGGACAAAGGGAGAGAATCCATTAGAGCTGCAGTGGCAAAAGCAGTTCTACAGTTAAGAGAGCTAGGTGAAAATGAAATTGAAGTAGACTCTTGCGGGGACACTGAAGCTTCTGCAGAGGGATGTCATCTAGCGTTGTTCTCTTATGATGACCTGAAGGCCGAGAAAAGTCGAAAGCCAGCAGTCAGGATTTCTTGTGCAACACGCTACAGCCAAGACAAAAACAGCATGGAAAAAGAATGGAGAAAGGGAGCAATTTTAGCAGAGGGCCAGAATCTCTCAAGGCGACTAATGGAAATGCCAGCTAATCTTCTTACACCCACAAAATTTGCAGAGATCGTCAAAGAACAACTGGCTGACAAGTGTGAAGTTCTGGTCAGGGATAAAGACTGGGCGGAATCAATGAAGATGGGATCATTTTTATCAGTAGCTAGAGGATCGGTAGAACCTCCTGTATTCTTGGAAATTGAGTATAAAGGGAGACAATCGGACAGCCCTCTGGCTCTAGTTGGGAAAGGAGTCACTTTTGATACTGGAGGAATCTCTATCAAGCCTTCCCAGGGCATGGATGCCATGAGGGGGGACATGGGTGGGGCTGCCTGTGTGGCGGGCAGTCTCCTAAGTGTCAGTAAACTACAGCTACCTGTTCATGTCAAAGCTTTTATACCATTATGTGAGAATATGCCAAGTGGCTCAGCAACTAAGCCTGGGGATGTAGTTACTGCAATGAATGGGAAAACAATACAGGTAGACAACACTGACGCAGAGGGACGACTTATTCTGGCTGATGCTCTGTGTTATAGTGAACAGTTCAACCCTTCCCTCATCCTAGACATGGCAACTCTAACAGGTGCAATAGATGTTGCTCTCGGGGCAGGTGCTGCTGGTGTTTTCACAAACTCAGAAAACATGTGGAACAAACTGCAAAAGGCCAGTGTAAGATCTGGGGACAGAGTGTGGAGGATGCCACTGTTCAACCATTACACAAAGAAAATAACAGAATGTCAACTAGCCGACCTTAACAACATTGGAGGGTCAAGGTCGGGTGGAGCCTGTACAGCAGCCGCCTTCCTCAAGGAATTTGTAAACAACAAAAACTGGCTTCATCTAGATATAGCTGGTGTAATGTCCAACAGTGGAGATGTAGCGTATCTAGGGAAGGGCATGTCAGGACGACCAACTAGAACTGTGATAGAATTCATCAACCTGATGAGTAAAGAAACCAAGAATTAATAAAATTATATTTCTATAGATGTCAGTTGTATTTAATTGTGTGATTCAAAGATGAACTTTGAGTTGTATCACGATATGATTGATGTTTGCATGTGTGTGAAAAATAAAAAATAATAATGCCTCTCAAAAAAAAAAAAAAAAAAAA AF137051 ATCACTAAGGGCAGGAAAAGAAACTAACTAGGATTCCCCTAGTAACGGCGAGTGAAGCGGGAAGAGCCCTGCACCGAATCCCTCATCCTAGCGATGCTGGGAACTGTGGTGTTTGGGACGTCTGTTGTGGTCGTGTGCCGGAGCCCAAGTCCTCTTGATTCGGGCCATCTACCCAGTGCGGGTGTTAGGCCTTTACTGGCTTCGGCCTCGGCTGCTCTGGACTGTCCTAGGAGTCGGGTTGTTTGAGAATGCAGCCCAAAGTGGGTGGTAAACTCCATCTAAGGCTAAATACTTCCCCGAGTCCGATAGCAAACAAGTACCGTGAGGGAAAGTTGAAAAGAACTTTGAAGAGAGAGTTCAAGAGTACGTGAAACCACTTAGAGGGAAACGGGTGGACCCGCAAAGTCGGCCCGGAGAATTCAGCTCGTCGGAGGGCAGTTGCGGTGTGACTCGCAGGGGGCCGTTCGCGGTCAACGCTTGTCGCTGCTGCGATCTCGTTCGACGACGTGTGCACTTTCTCCGGGCTCGAGCGCCACGACCGGTTTCTATCGGCGGTCAGAAGATCTGGAGGCAGGTGGCCCGCCGGCGGACTCGTTTCCGCCGGTTGGGAGTTATAGCCTCCGGAACGCGGGCCGTCGCGAGACCGAGGACCGGCCGGCCGCTCTTCGCTCCTGTCCTTGCGTGCACGTTTCGACCTGCGGATACTGCCTCTCTGGGGCAGTGGCCGCTAACCGCGTCGTGCGCACCGGACCGGGATGCGTGGGCTGTGCCCGATGGTCAGTGGCGAATCGGTCGGTAGTCCACCCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGTGCGCAAGTCATTGGGTGTTACGAAACCTAAAGGCGTAATGAAAGTGAAGGCAGCCTCGGGTTCTGCCTAGGTGG AF204062 TGCTTGTTTCGATGTCAATCGGATGACTTTAATTTCTTGTCTGCCTCATCTTTTACTTATGGGCAATCTTCTAACCCTCCAAAATTACAAACATTTATTTTTTTTTTTACCTTAACTAGATTAAAATCCCAAAAATATCAAGTTGTTCATTTGAATTGCATATGGTAGCGATTTACTTAAAGTCGTACAAAAAATTACCGAAATGTGTATTGTCAACGTTGTGTTATCAGAGTCTGATAAATCGTCACGTAAATGCTTGTGACCTCAAAACGAGGCTTACCAAAATACTGGTATTAAATTTGATTGGTTGAAAAAATCACACGTCCAATAACATATTTGTGCAAAGGTTGAGGAAATTCTATTGGAAGGTTTTTTTTAATTTACTAGAAAATTGAAATGGAGTGCACACACACACATACATGTATACATACATACATACATGTATACATACATACATTCATACATACATACATACACACATATAAACACACACATGCATGGTAGCGATGCTGTTAG AF204061 CTTGCCATATTGCCATGTGTGTGTGTGTGTGGGGGGGGGGGGGGGGGTCAAAGTCACCACTCGACGTAATTCGATGCCTTATGTGTTAAGTATCCTGTTAGGTAAATTTTCATTCAAGTAAGAAGTACCTGTGACAATTCCATGTAAAAGCCCTACCAATGATTGATACATGTAATTTAAAGATCCAGCATAAAATTAGGAACTTTGAATTATGTCATTAGGTACAAATAAAATGTATGCTGTTCTTTTCTTGTTATCTTTTTATATGAGTATTAGGATGAGAGGGAGATAAAAACGATCTTGGTATATCCACTGAAAACTTCTTATTTCGTACACCAATTTGCACCATCTATGCAAAGATATAGTATCAAAATCCTTNTTCTGCGTATGAGCAGAAAAAAAATAGAACTCGACGCCATAATAATTATACACACCTACA AF204060 CTACAATTATCATTAAGGATCCGTCGACAAATCCAAAATATCCTTTTACATTTGGTCAAAAATATATGCTTATCAATACTAAATTGGCTTCTTTATTTAATGAGACCTATACAGTGAGTGTTTGCTCATTATATTATCACAAGGTTAGCGTCCAATTACAGCAATCGGGTTTATCAATACAACATAACTTTACCATTTGCACCTTTCCAACGTATATAATGTTTGTCCCTCTCTCGCTCTCGTCCTCCTTCTCTCTCTCACATACTCTCACACACACACACACACACTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTATGTCACTTTTTCTGTTTTGTTTTCGTGCAAGGCTTCAAGTGTCATTTTATATTAACCTTTCTTTTAAACAGCGTCAAAAG Crassostrea AGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAACAAAACAAATCGGGGCTCGTTGGCAGAGCGACCGAGAGGCTAACGCAAAAACACAGCCGAGGGTTGTTGTTAAAGTCGGATCGACCTCGAACGCCCAGCGACCAGGTCGCTAGGCCGAGGGATCCAGGCGAACTCGCTGGAGGGTTTATCTCTCAGCGCCTTGGGCCGTCGAAGCTTTCCTGCTCCGTCGCCTTAAGTACAGACGAGCTCGACCGCGACCCCGGGCTTCCGGAACGGTGGGTCGCTAAAACAAAACAAAAAGCACTCGGCATCGTCGGGGGGAAACCTCGACGTTATAAGCACCCGAGTATGTACTTTCTCACGTATACCAACAGATTTCTTACACAAAACCCGGGAAGGCGGAGTCGGCAAGGCTCTTGCCTTTTTTCGGGGGTCGGCCGGCGTACCTCGTTGCGCGCCGCGACCGACCGAATTGGCATCATACTATTTTGACAACTCTAAGTGGTGGATCACTCGGCTCGGGGGTCGATGAAGAGCGCAGCCAGCTGCGTGAATTAATGTGAATTGCAGGACACATTGAACATCGACACCT AF051183 CTAGACGCCTACCGAATCCACATTCGATAACTGTAGTGGGGGGGGGGGGGNGNGTTGTTTGAAANAAAAACGTNAAAGGGGCCCTTTTCCTTATNNGNNGAATNCGCCAAANTNAAAANAAAACCGTTTNANTTTAATTTTAAAAAANGGTTAAATTGGTTTAAAACTTTTTTTTTTTTTTTTTTTTTTANCCNGAANCCTTTTTNTNTTCTTTTTTTTNTNTNTNTNTTTTTTTTTTTTTNTNTCTGGGGGGGGGGGGGGGGGGAAAGNATATTTTTTTCCAACCCTGNNAGANTGNGGGAANGTANAAAAGGGTAAANNCCCCCANNNTNNTNTTGGGGGNCCCNNCGCCCTAANGTTAAAGGGGGAANNGTTNGGGNNGNNGGGNCCCCCCCCCGGNCCAGGGGANGGGNANNAAAAA
#uploading to SQLSHARE
!python {spd}singleupload.py -d Cgigas_EST_Nuc_NCBI_040414_cl /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab
processing chunk line 0 to 151942 (2.43243002892 s elapsed) pushing /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab... parsing CC484ED9... processing chunk line 151942 to 207445 (201.518175125 s elapsed) pushing /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab... ^C
!python {spd}fetchdata.py -s "SELECT ProbeName,GB_ACC,Column2 as sequence,Description FROM [sr320@washington.edu].[GPL11353_array]ar left join [sr320@washington.edu].[Cgigas_EST__Nuc_NCBI_040414_cl]est on ar.GB_ACC=est.Column5" -f tsv -o /Volumes/web/cnidarian/GPL11353_fasta2.tab
Traceback (most recent call last): File "/Users/sr320/sqlshare-pythonclient/tools/fetchdata.py", line 77, in <module> main() File "/Users/sr320/sqlshare-pythonclient/tools/fetchdata.py", line 71, in main data = fetchdata(args.sql, args.format) File "/Users/sr320/sqlshare-pythonclient/tools/fetchdata.py", line 30, in fetchdata return conn.download_sql_result(sql, format) File "build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py", line 328, in download_sql_result File "build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py", line 252, in poll_selector sqlshare.SQLShareError: code: 400 : {"Detail":"Invalid object name 'sr320@washington.edu.Cgigas_EST__Nuc_NCBI_040414_cl'."}
!fasta_formatter -h
/bin/sh: fasta_formatter: command not found
cd /Volumes/Bay3/Software/
/Volumes/Bay3/Software
ls
.DS_Store ._.DS_Store ._novocraft* ._novocraftV2.07.10.MacOSX.tar.tar.gz ._samtools* ._sratoolkit.2.1.0-mac64* ._sratoolkit.2.1.0-mac64.tar.tar.gz Anaconda-1.4.0-MacOSX-x86_64.sh Anaconda-1.9.1-MacOSX-x86_64.pkg BEDTools.v2.17.0.tar.gz BSMAP/ BisSNP/ Blast2gff/ CePa/ CePa_0.5.tgz DESeq/ DSG-0.1.0/ DSG-0.1.0.tar EMBOSS-6.5.7/ EMBOSS-6.5.7.tar FastQC/ FastQC.app/ IGVTools/ IGV_2.3.3/ IGV_2.3.31.app.zip IReckon-1.0.7.tar IsoEM-1.1.1.zip LTR_FINDER.x86_64-1.0.5/ LTR_FINDER.x86_64-1.0.5 2/ LTR_FINDER.x86_64-1.0.5.tar.gz MITE_Hunter/ MethyQA.v2/ MethyQA.v2.zip MotifLab/ MotifLab.zip NCBI Blast/ PyML-0.7.11/ PyML-0.7.11.tar.gz QSPEC_V2/ QSPEC_V2.zip Rad_perl_pipeline/ RepeatMasker/ RepeatMasker-open-3-3-0-p1.tar SOAPdenovo-Trans/ SOAPdenovo-Trans_1.01.tar STAR_2.3.0e.Linux_x86_64.tgz STAR_2.3.0e.OSX_x86_64/ STAR_2.3.0e.OSX_x86_64.tar SpliceGrapher-0.2.2/ SpliceGrapher-0.2.2.tgz SplicingCompass/ SplicingCompass_1.0.tar.gz WUBLAST/ __MACOSX/ abyss-1.3.4/ abyss-1.3.4.tar.gz ap11_samifier-master/ ap11_samifier-master.zip bedtools-2.17.0/ bg/ bin/ bismark_v0.6.4/ bismark_v0.6.4.tar.gz bismark_v0.7.12/ bismark_v0.7.12.tar.gz blast3_pe/ bowtie/ bowtie-0.12.7-macos-10.5-x86_64.zip bwa-0.6.2/ bwa-0.6.2.tar.bz2 cd-hit-v4.5.4-2011-03-07/ cd-hit-v4.5.4-2011-03-07.tgz circos-0.56/ circos-0.56.tgz clc-ngs-cell-2.0.3-mac_64/ clc-ngs-cell-2.0.3-mac_64 copy.zip clean_reads-0.2.3.tar.gz cnv_blast2cnv/ combinedCG_MBDgill_oysterv9_5x.bed diffsplice_0.1.1/ diffsplice_0.1.1.tar distribute-0.6.35.tar.gz distribute_setup.py eRNA_v1.01/ eRNA_v1.01.zip ea-utils.1.1.2-537/ ea-utils.1.1.2-537.tar.gz emboss-explorer-2.2.0.tar.gz fastqc_v0.10.1 (1).zip fastx_toolkit_0.0.13_binaries_MacOSX.10.5.8_i386.tar.bz2 fink/ genometools-1.3.9/ genometools-1.3.9.tar.gz gephi-0.8.1-beta.dmg get-pip.py gmap/ gmap-gsnap-2012-11-09.tar.gz go-perl-0.13/ go-perl-0.13.tar.gz iReckon/ igvtools_2.3.31.zip iprscan/ ipython-master/ ipython-master.tar.gz irods3.2.icmds.mac.intel/ irods3.2.icmds.mac.intel.tar isoem-1.1.1/ jbrowse-1.2.1/ jts-sga-bb2f0ea/ jts-sga-v0.9.20-5-gbb2f0ea.zip khmer/ matplotlib-1.2.0/ matplotlib-1.2.0.tar.gz methVisual/ methVisual_1.0.0.zip minia-1.4683/ minia-1.4683.tar misopy-0.4.7/ misopy-0.4.7.tar.gz msatcommander/ msatcommander-0.8.2-OSX.dmg ncbi-blast-2.2.26+/ ncbi-blast-2.2.27+/ ncbi-blast-2.2.27+-universal-macosx.tar.gz ncbi-blast-2.2.28+/ ncbi-blast-2.2.28+-universal-macosx.tar.gz ncbi-blast-2.2.29+/ ncbi-blast-2.2.29+-universal-macosx.tar.gz novocraft/ novocraftV2.07.10.MacOSX.tar.tar.gz novocraftV2.08.02.MacOSX.tar.gz pass_v2.0.tar.gz pbcore/ pbh5tools/ pbh5tools-master/ pbh5tools-master.zip phobos-v3.3.12-mac/ phobos-v3.3.12-mac.zip priority.2.1.0.zip qprot_1.2.2/ qprot_1.2.2.zip rmblast-2.2.27/ rmblast-2.2.27-universal-macosx.tar.gz samtools/ seqmonk_v0.20.0.dmg splign splign.gz sratoolkit.2.1.0-mac64/ sratoolkit.2.1.0-mac64.tar.tar.gz stacks-0.9999/ stacks-0.9999.tar.gz tablet_macos_1_12_02_06.dmg* tophat-2.0.6.OSX_x86_64/ tophat-2.0.6.OSX_x86_64.tar.gz tornado-3.2.tar.gz trf* trf_data/ trinityrnaseq_r20131110.tar.gz usearch usearch5.1.221_i86osx32 velvet_1.1.07/ velvet_1.1.07.tgz
!wget http://dl.dropboxusercontent.com/u/115356/docs/annotable/Roberts_Sigenae6_transcriptome.fa
--2014-04-04 12:05:10-- http://dl.dropboxusercontent.com/u/115356/docs/annotable/Roberts_Sigenae6_transcriptome.fa Resolving dl.dropboxusercontent.com... 54.225.207.37, 54.243.164.243, 54.225.246.188, ... Connecting to dl.dropboxusercontent.com|54.225.207.37|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 25210642 (24M) [text/plain] Saving to: `Roberts_Sigenae6_transcriptome.fa' 100%[======================================>] 25,210,642 887K/s in 28s 2014-04-04 12:05:38 (890 KB/s) - `Roberts_Sigenae6_transcriptome.fa' saved [25210642/25210642]
#tab delimited version
!perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' Roberts_Sigenae6_transcriptome.fa > Roberts_Sigenae6_transcriptome.tab
Converted 31952 FASTA records in 451733 lines to tabular format Total sequence length: 24247683
!head Roberts_Sigenae6_transcriptome.tab
AJ565441.p.cg.6 GCTGTCGCTCTAGATAACATTTCCAAGTACATGTACATATCTAGCTGACCTGACTTATTTTGCAAGAAAGGAGAACAGAGTTCGAATTACAGATTTTGGATATGACCTGCAGGGATGGAAAAGCATTCTTCATATTTCTTGCCGTGGTGACAGTAATACCCCAGAAGTCGGTTCAATGGGACCCGGATGCTGGTATAGTGACGTCATGGACAAAGTATCCGAATGTTACAGTAAACGTATCGTCCTCTTCCGGCACATCTGATCCAAGATCAGTAGTGGATGACAACGACAACACAATGTGGGTTTCCGGAAGCTGCCTGCCGAGTGGCTTTGTGGGTGACCCAGAACTGAACCTGTTCCATGGTCTTTGTGACAATAACAATTTATGCTCGGTGTCAAATAGTCCCGATATTTACAAAGCGACTGATGGCAACCCATCTTACACTGTAGCTACAATTAACCCCGGACAAGATTCCTCCGAGGCCAAGTTAGTGATTAGTCTACCTCAACCCGAGGTGTTGATGTTTCTCACTGTCTGGGGTATATACAACCACGGTACTACCAAGATGTCTTTGTTTGACAGTAACAACATTCGACGGGATACAAGGTTGCTTGTATCCGCTGATAGCTACAAACAAATTTCGCTTACCAACATTTCTTACGCTGTCGCTAAGATAGAGTTTAATTCTAGTCAACAATTTCAAATCAAGGAAGTTGCTGCTCTTGGGAGCAAGGGATGCATCGCCAAACTGACACTGGATCTCGGGGACACACGTATGATTCAAACAATTCGATCACGACATTGGGCTGGACATAACACAGCCTCTGCCTTAAAATTAAAGATTTCTGAATTCGGAAA AJ565444.p.cg.6 GTACGTAATTGCTGTTTTGTTTTAAAACAAATATTTGTTTAAATTATCAAAATAGGAGAATCGATTAAACCCAGATGCTTTCCGTCGGAGACAGAATCAAAAACTGTGAATGTAACAGAAGACAAACCAGTTGGGTTCACCGTGTTCACTTATTCGGGTTTTGATGCTGATGGAGATCGCATTAGATTTGTGTTACTTGATAACACGGTGCCGTTCTCGATTCCAACAGCAGGATCCGGGGATGTTGATGTGGCTTTACCTGCCTTAGACTTTGAGAGGAAAACTCAATATATTTTGGACAAAATATACGTCACTAAATTTGGATTGAGTGCACTCCTGTTTGGTAATAAATGTGGAACCCTAACCGTCAATGTCCTCCCTGTCAACGAATTTACGCCAGTTTTTGATCCCTCATATCAAAATTCCTCACTTCCAGAAGGTCTACTACAAAATTCATTGCTTGCTAAACTGAATTGTTCTGATGAGGACAAAGAACCCAACGAATCCCCTTTTGGATGTTCATCAATAACTATTCAGACTGGAGATGACATTAAACCGAAATTTACGATAGTCAACAACGCTGTCGTCACAACAAACAACGTCATTGATTTCGACACTGGTGACGTCATTTACACACTTGTCATAGTTGGTGGTTGATAGTTCAACACGTGATCCACGTAAAACAGGAACGATGACGATAAAGGTCATCATTGAACCTGTG AJ565448.p.cg.6 GGTTATTTGCTACTCTTGACAGCCCGGTTGACGAAAATCAAACACCAAGTGTACTGAGACTCTTGTCTAGACCGATTTGTGGGGTCAAGGTAAATTAGATGATCCTCTATACAATGGATTCATCATTGTCATTTAAGCACCAAATTTTTATTGGAATAAAGATTGTACATCATTTTACTAAAATGGTTCACAAAATAACCTATTTATCAAGAATTTATTGCATATTTATACTAATTAATATTTGGATAACCACATGAACAAAATGAATCAGATTTAAAATTGTTCTAAAAGTATTCAACTTTCAGTTAAAATATTTATTTATATTATATTTAAACATTGATTTTTAAGCAAAAAAACTCAATAAAAGAACTGTTGAATACAACATGAGAGTAACTGAAAATTATTGATGTTAAGGATGTCTGGGATAAACAAGAGGTCATTAAACATTATTCGGACACTAAATTTCACAAAAGATTATTATTTGGTATTTATTACAGACAATTTGACTTGAAAATTTATTTTGAATGCTAATTCAGACCAGAGTATAAATTGCACATCATTTTGATTTTAAATTTAAATGCTGAACTGCAGGATGAGGTTAATGATGACTATTTGCTACTCTTGATGTCACACTGATGTCAACTATCACCATTTTCTGAGATCTCATCTGTAGTGTATG AJ565449.p.cg.6 ACCCAAACACACAGCCCATCTTCTTCTCAGAAGGTTTCCAGATGAATTCAATTTCACTCACAGTTCTGCTGCTCTGCCTGTTTGCAATCAGCATAGCGGCCGGATGGTGGGTTGAAGGAGAATTGGACCTGTTCATAGCGAAAGCAAAAGTTGGTTTTCTTTTTAAAGGCAGGAGAAAGAGGCATATTGCAGAGGAACAAGTCTTTAACGTAGTGATGTTCATGGTAAACGAAAAAACCGGAAGTAGATTTAGACTCAACCCATGTGACTATGCGCTATATGACCAAGACGACGACTTCACGGTCACGCCGAAAGATTTTGATATAATATTCTCTAAAATGGATAAATCAAAACATATTTTGGTGGAACAGCTTTTCCGTGAATTGGATATGGATAATGATCAGAAAATTTCCCTAACGGAATTTGAGGAAAAAGAAGGTCTTGTTTTCTCCAAAAAGACGTGCCTTATTGACGTGTTATATTCATGACTTTTTTCTGTGTTTTCTTTTTTTTTTTTTTTTTTTTTAAAGTAAAATTGATTATTATTTGTTCTAAAACGAATTATCGTATTCTAAAAAACCTGTGTATCTTATTATCAATTATTATCATTCATATATTTGTTTCATCTGGAATATCGATATATGTCCGTGAAATACATGCCTTTTTGTCATTTTTGTACTC AJ565453.p.cg.6 GGACTCCCTCTAGATCTTAGCATGAAATAAGCTTAGCTAATGCATGATCTTGTTTTTGTATATGCCTTGCAATATTATGTAGAAATAATCAATGTGATTGAGCATTTTGGTGTGAATAATTGCATGAATTGTTATATCATAATCTGTAATTTCACCATTAAAACTAGTGCTCTACTC AJ565458.p.cg.6 GGGTGGAATATTTGTTGGAGCATTTCTTCTTCTTTCCTTTATCTCGTTGGTGAAAGGAAACTGTTCTTTTTCCCGCAACTTGGCTGGAAACTGGGTAATAGATAAAGATGGAAAGGAACTTGGGCGCATGTCGATTGGCTACACAAGAATGGACGTGAATTTTATGGGCCAACGATACAACTACACCTGTAATCAATTTGACTACAGTGAAGAAAAGTATCTACTGAGGGCTACAAATGGGAATGGGATGGCATGCCTGTTATTCACACAGTTCAGTGATGGGGGCTCCACTCTTATGATGATCCGTCTGCACATGACCCACCACTATGAAGATAAGAATTTCTTCAAGCCCCAACAAGTAGCGGGATCTCCAACCATGAACTCAGTGTGTAACAATTATGACGATGGACAAATGCTGTTTATTCACTCTGTGCCCTGAATTGTCTTACATTATTCTTACATTATTCTTGATTGTGTTTGATATATTTTTAGAATTATCTGTTGCACATAGACTATAGAAAACACCTGTTTATATTTTGAAATTTAGCCGACAATAAAGTATGGTTAAATATGTTTTAAAGACAATAAAGAAAATGATTTT AJ565465.p.cg.6 GCACAGACCAAGGATCAGCACACTGGAATCAGCTGTTAGTGGAGATGGACGGCATTAATACGACAGAAGGAGTGATTGTGCTGGGGGCCACAAACAGGGTGGATATATTGGACAAGGCCTTGCTACGTCCAGGAAGACTTGATAGACATATCCTTATTGACCTCCCCACATCTGAGGAGAGAGTGGAACTCTTTGAAATGTATTTGTCAAAGATTAAAATAGACTTCTCCATTTCTGTATTTGCACCACGACTAGCACAGCTTACACCCGGAATGTCAGGTGCTGACATTGCAAATGTGTGTAATGAAGCAGCCATTTATGCTGCGACCAACAACAAGGATCAAGTAACAATGGCAGATATGGACTACGCTCTACAGAGGATCATCGGCGGTCCAGAGAAGCGATCTTTTGTGAGAGACGCCCGCGAGAAAAAGATCAATGCGTACTACGAGGCAGGAAGAGCTGTGGTTTCGTGGTTGACCAGAACTTCTGATGCCATTTTAAAGATTTCAATTGTACCTAGAAGTAAATACAGATTAGGCCATTATCAGTATTATAAGCCGGAGAGGGATCTCCAGACTAATGTGCAGTTATTTGAGAAGATGCTTGTCCACTTAGCAGGCAGTGCTACAGAGGCTCTGGTTTTCAAGCACCATTCCACAGCTGCTGAAAAAGATCTGGATATTGTCAAAAAACTTGCTTACCTACAAGTTAGAGGAATTTGGAATGAATGAAAATGTTGGCCAAATCTCATTTCATTTCGAGGGAGGGGGATGAAACCCTCCCTAAACCCTACAGTAAATACATGGGAGAATATGATTGACACGGAGGCAAGAAATTTGGTTACAAAAGCTAGTGTGCAG AJ565467.p.cg.6 GGTTGGTGATATTTAGGAAAAGAGTGAAACAATTGTGGTGCTTAAAATGCATTCTCCTACATAACAAGAAAATGTCTTTCATCTGTATTAGCGCAAGATCAACGTTCAAGATATCCGCTTCAAAGCAAAACCATCGAAGAAACCACGCAGAGGTAGATGAATTACGAGGGCGAGAAAGAAAAAGCATCAAGAAAAAACTCGACAAGGGGCATTACTCTCCTATTAAATGAGGAGAAGAATCGAATCAAAGAACGTCATCGGAACCCCAGCAGTGACACCAACTTTTCGAACTCAGATGCGGGAAAAGTAAGGTTGGAGACAGAATGTCTACAAAGCAAACAAAATGGCGTCCGTGGAAACTCGTTAAAGGAATCACTAGATACCATATCAAGATATACCGGAAGCTTTGAAGAATTTGTACAGAAAGAAATATCATCAAATAGAGATCTAGAGAACCAAGCACATTCATTAGCATCACCATTGTGTCATTCCATGAACATGGAGTTAATCCGACTCAGGTCTTTCCATAATTTCCCGTCCTCAAAAACTATTTCTACACTGCGACTGGCTCGCAAGGGATTTTATTATTCTATGGAGTATGACGTCACAATATGTTTTGCTTGTGGTTTTCGAAAACGAGACTGGAGGTCTGACGATGTCATTGAGGTTATTCATCGTAACATGTCTCCTGACTGTCCCCTTCTGTCAGCACAGCCGACCAGTAACATCCAAATTGGAAATGACCAAAGGGATGGGCATTGTATAAACGAACTCGAGCAGCAATTTAACGCTAGTGGTAACGAATTTCCTAGGAGAAGCAATAGACAGCCATCCCTCTTCAACCTCAGAAATGCTTCGTCTGGACATG AJ565474.p.cg.6 ATATAAAGCAGGGATCTGCTCAGGAAATTGCAGCCTGTAGAGAGATCCTCATCTCTTCGCATTGAAAGGCCAACTTCACTTGTTATTCGACAACACAGAAGAAATAGCCTGCCTAGTCCTTCTGTTATCAAGGCAATCGTCCATATACCGGACTTGGAAAGAGTCCGGTCTTTTAGTCTTACTCGAGACGGACTCAAAAACTGCGGGGACAAAATCAGGCGACGCAGTACATATAGTATTGCAACAAGTGAGGGGCCTGATTCACTTTCCACCGGAGCAACATCTTCTTTGGAAAGCATCTGTCAGAGGCAACAATTTAAGGTTGCTATCATAGGATCTGCAGGAGTTGGAAAAAAATCGTTGAAAAATCAATTTGCAACTTCAGAAGAACTTTACATAAACAATAAAAGTAAGTAAAAAAAAAGATTGGTAAATATTTCCGTTTATCATTTATCATTTAAAGCTATATGCGGCATATTTTTTCATGCTAAGAAATATTTGATTGATTTATTTATTTAAATATGTTATATAAGATATATCTTCACAATAAATTACGCAGTTTATATCAATCGGGATAAAAAGATATAGAAATTAATAAATAATTTTTAAAATTATTTTCGATTCCACGATAAATAGAGCATTTGAATAAACCCCGCCTTAAATCGGCCACGTGATACCACGAAATTTTTGAATAAAGAATAAATAAAAACTCTCAGTACATGCATCCCTCAGGAAGAGGGTGTATTCATAAATTTTATCGTGTCGTTGATGC AJ565485.p.cg.6 GCTTCAATCAGAACAAAGTATTATATTTAGATATATGTTGAAATGTTTAGGAATTAGTATTAATTTAAATTATAAATTATAAAAATAAAGAAGTAATACAATG
!python {spd}singleupload.py -d Cgigas_Sigenae_v6 Roberts_Sigenae6_transcriptome.tab
processing chunk line 0 to 31952 (0.137900114059 s elapsed) pushing Roberts_Sigenae6_transcriptome.tab... parsing C6E51C88... Traceback (most recent call last): File "/Users/sr320/sqlshare-pythonclient/tools/singleupload.py", line 42, in <module> main() File "/Users/sr320/sqlshare-pythonclient/tools/singleupload.py", line 39, in main conn.uploadone(args[0], datasetname) File "build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py", line 181, in uploadone File "build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py", line 202, in upload_chunk File "build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py", line 244, in poll_selector File "/Users/sr320/anaconda/lib/python2.7/httplib.py", line 1045, in getresponse response.begin() File "/Users/sr320/anaconda/lib/python2.7/httplib.py", line 409, in begin version, status, reason = self._read_status() File "/Users/sr320/anaconda/lib/python2.7/httplib.py", line 365, in _read_status line = self.fp.readline(_MAXLINE + 1) File "/Users/sr320/anaconda/lib/python2.7/socket.py", line 476, in readline data = self._sock.recv(self._rbufsize) File "/Users/sr320/anaconda/lib/python2.7/ssl.py", line 241, in recv return self.read(buflen) File "/Users/sr320/anaconda/lib/python2.7/ssl.py", line 160, in read return self._sslobj.read(len) socket.error: [Errno 54] Connection reset by peer
!head /Volumes/web/cnidarian/GPL11353_v6fasta.csv
!awk -F "," '{print ">"$1"\n"$2}' /Volumes/web/cnidarian/GPL11353_v6fasta.csv > /Volumes/web/cnidarian/GPL11353_v6fasta.fa
!tail /Volumes/web/cnidarian/GPL11353_v6fasta.fa
>AM860865.p.cg.6 >AM869341.p.cg.6 >EE677551.p.cg.6 >AM860135.p.cg.6 >BQ426856.p.cg.6
!head /Volumes/web/cnidarian/BiGoRNA_array_v6_tab
"Name" "Chromosome" "Region" "Expression value" "Gene length" "RPKM" "Unique gene reads" "Total gene reads" CU995582.p.cg.6 CU995582.p.cg.6 1..1092 4 1092 0.236 4 4 AM862909.p.cg.6 AM862909.p.cg.6 1..595 0 595 0 0 0 CU991229.p.cg.6 CU991229.p.cg.6 1..1230 148 1230 7.767 146 148 AM863560.p.cg.6 AM863560.p.cg.6 1..562 101 562 11.601 101 101 AM868645.p.cg.6 AM868645.p.cg.6 1..462 2 462 0.279 2 2 AM856822.p.cg.6 AM856822.p.cg.6 1..846 0 846 0 0 0 FP006184.p.cg.6 FP006184.p.cg.6 1..287 16 287 3.599 16 16 AM862004.p.cg.6 AM862004.p.cg.6 1..808 132 808 10.545 132 132 CU998134.p.cg.6 CU998134.p.cg.6 1..1001 772 1001 49.783 772 772
!head /Volumes/web/cnidarian/BiGoRNA_array_v6_tab.txt
ID Sig_No Gene length RPKM Unique gene reads Total gene reads CU995582 CU995582.p.cg.6 1092 0.236 4 4 AM862909 AM862909.p.cg.6 595 0 0 0 CU991229 CU991229.p.cg.6 1230 7.767 146 148 AM863560 AM863560.p.cg.6 562 11.601 101 101 AM868645 AM868645.p.cg.6 462 0.279 2 2 AM856822 AM856822.p.cg.6 846 0 0 0 FP006184 FP006184.p.cg.6 287 3.599 16 16 AM862004 AM862004.p.cg.6 808 10.545 132 132 CU998134 CU998134.p.cg.6 1001 49.783 772 772
spd="/Users/sr320/sqlshare-pythonclient/tools/"
#uploading to SQLSHARE
!python {spd}singleupload.py -d BiGoRNA_array_v6 /Volumes/web/cnidarian/BiGoRNA_array_v6_tab.txt
processing chunk line 0 to 31918 (1.10805797577 s elapsed) pushing /Volumes/web/cnidarian/BiGoRNA_array_v6_tab.txt... parsing F8132D65... finished BiGoRNA_array_v6
!python {spd}fetchdata.py -s "SELECT * FROM [sr320@washington.edu].[BiGoRNA_array_v6]rna left join [sr320@washington.edu].[GPL11353_array]arr on rna.Sig_No=arr.ContigName" -f tsv -o /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt
!head /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt
!python /Applications/q "SELECT * FROM /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt WHERE c1 like CU995582"
query error: no such column: CU995582
!grep "CU995582" /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt
!head -3 /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt
!egrep -wi --color 'CF369228|EF219426|EF219427|EF219428|EF219429' /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt
!egrep -wi --color 'CU998852' /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt