{ "metadata": { "name": "", "signature": "sha256:9718c252c1767fd29c6d0a36a54d98c7403d830869635f62c5fd4ea313c2c245" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Dheilly et al : Resources associated with Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "quick links \n", "- [RNAseq join array](#BiGo-Sperm-RNAseq-v-GPL11353-array) \n", "- [Supp data from Dheilly et al](#Supplementary-tables-from-Dheilly-et-al)" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Array Design" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"SQLShare_-_View_Query_18EEEE73.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [ "file=\"/Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_b.fasta\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "!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" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "Converted 206388 FASTA records in 2488079 lines to tabular format\r\n", "Total sequence length: 138128102\r\n", "\r\n" ] } ], "prompt_number": 14 }, { "cell_type": "code", "collapsed": false, "input": [ "!head {file}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">gi|318053987|gb|FQ662477.1|FQ662477 FQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence\r\n", "GGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTA\r\n", "CAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTT\r\n", "ATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAG\r\n", "ATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACA\r\n", "ATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCC\r\n", "TACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATA\r\n", "AAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGAT\r\n", "TAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATT\r\n", "ATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTT\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"AM863560\" {file}" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "1\r\n" ] } ], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "#Translate pipes to tab so SPID is in separate column for Joining\n", "!tr '|' \"\\t\" /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "spd=\"/Users/sr320/sqlshare-pythonclient/tools/\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "#uploading to SQLSHARE\n", "!python {spd}singleupload.py -d Cgigas_EST_NCBI_040414_cl /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 122527 (0.58825802803 s elapsed)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "pushing /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing 54E9735E...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 122527 to 206388 (163.788265944 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing 7C0B8204...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished Cgigas_EST_NCBI_040414_cl\r\n" ] } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "!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\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/GPL11353_fasta.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ID\tRow\tCol\tProbeName\tContigName\tGB_ACC\tDescription\tSEQUENCE\tColumn1\tColumn2\tColumn3\tColumn4\tColumn5\tColumn7\r\n", "43070\t507\t60\tCUST_23696_PI419289827\tFP010368.p.cg.6\tFP010368\t\tGCAGGCTTACATTTGTTATAACTTGGTGAGGATGGTAAAGGGAAGGTTAGTGTATATTTT\tgi\t260935343\tgb\tFP010368.1\tFP010368\tGGGCAGAGATTTCAGTGACTTTGAAGTTAAAACAAAATTTTCTTCGGACACTGTGACACTAATGATTTATGTCTTTGTGTTTATATTAACAATTTTATAACAATACCTCAATATCTTATTCAAGATATTTCGGTTTTGGGGTGGGGGGAGTGTGATAGGATTATATTTATCATGATCACATGAAAAGCACATGTTCGTCTATAGCTTTAAGCAAAACGTAACGATAAATATGATTGGTTGTACTTGTACTCGTTTAATTTACATTCGGAAAGTGTCGGTGTCATTCATAATAATTTGGGAAAATGCTGGTTTGAGTTATAAATACATATAGTCGTTCTGATTGGTTAAGAGAAACACACCCCCAGAGCGCGGTGTATACAAAGTCAGGATTTGCCTTAGTCCGGCAGTTGACGTGGAATCTTCTCTAAGGTTCGAGTCAACTCACTTCCCCGGGTAGATGGGTGGGCCCCAGTCTCCATTTCCCGTCTCGTTCATCGTCTCGCTAAGTGTTTTGTTTATTGTCCTGTAAATGTCCATTGTGCAGCATGCTAGGCGTTTAGTCCGTGCTAAGTCAGGGTTAGCATTAGGTTTGGGTTACTTGGATTTTTATTAATATTAAGGCAGGCTTACATTTGTTATAACTTGGTGAGGATGGTAAAGGGAAGGTTAGTGTATATTTTTGTATATATATAATGTTTTTGTACCCTGTTTCATGCACCATAATAAATCTATAAAAACTCACC\r\n" ] } ], "prompt_number": 46 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print \">\"$1\"\\n\"$2}' /Volumes/web/cnidarian/GPL11353_fasta.txt > /Volumes/web/cnidarian/GPL11353_fasta.fa" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 54 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/GPL11353_fasta.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">AY039650\r\n", "(sp:O73823)\r\n", ">AJ496218\r\n", "\"(sp:P08906)\r\n", ">AB289857\r\n", "(sp:P97481)\r\n", ">AJ971237\r\n", "(sp:Q13231)\r\n", ">AB307634\r\n", "(sp:Q6L6Q6)\r\n" ] } ], "prompt_number": 55 }, { "cell_type": "markdown", "metadata": {}, "source": [ "Some are not ESTs\n", "\"Screenshot_4_4_14_8_51_AM_18EF0C86.png\"/" ] }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "Lets cat the Nuc and EST files" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!cat /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_b.fasta \\\n", "/Volumes/web/cnidarian/Cgigas_Nuc_NCBI_040414.fasta > \\\n", "/Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta \\" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 56 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \">\" /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "216622\r\n" ] } ], "prompt_number": 57 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", ">gi|2952502|gb|AF051183.1|AF051183 Crassostrea gigas clone BI57x G and T mononucleotide region\r\n", "CTAGACGCCTACCGAATCCACATTCGATAACTGTAGTGGGGGGGGGGGGGNGNGTTGTTTGAAANAAAAA\r\n", "CGTNAAAGGGGCCCTTTTCCTTATNNGNNGAATNCGCCAAANTNAAAANAAAACCGTTTNANTTTAATTT\r\n", "TAAAAAANGGTTAAATTGGTTTAAAACTTTTTTTTTTTTTTTTTTTTTTANCCNGAANCCTTTTTNTNTT\r\n", "CTTTTTTTTNTNTNTNTNTTTTTTTTTTTTTNTNTCTGGGGGGGGGGGGGGGGGGAAAGNATATTTTTTT\r\n", "CCAACCCTGNNAGANTGNGGGAANGTANAAAAGGGTAAANNCCCCCANNNTNNTNTTGGGGGNCCCNNCG\r\n", "CCCTAANGTTAAAGGGGGAANNGTTNGGGNNGNNGGGNCCCCCCCCCGGNCCAGGGGANGGGNANNAAAA\r\n", "A\r\n", "\r\n" ] } ], "prompt_number": 83 }, { "cell_type": "code", "collapsed": false, "input": [ "#tab delimited version\n", "!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" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "Converted 216622 FASTA records in 10632690 lines to tabular format\r\n", "Total sequence length: 706438140\r\n", "\r\n" ] } ], "prompt_number": 58 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "gi|318053987|gb|FQ662477.1|FQ662477\tFQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence\tGGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTACAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTTATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAGATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACAATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCCTACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATAAAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGATTAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATTATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTTTATGATCGAAAATGTTTTATTTCCTTTATTATTTATCTGGATATATTATCTGACTCTATACACAAAAGAAGCAAAGCTTTGATGCGTAGTACACATGTGCTGTCAGCCTCATTTTGGTGATGACAATCCAGTTCCTGGTCATCGGTGTGTTTGAAAGCTGCATTCTCCTCAATGTTGTTGGTTTAGCTTCAAGCAAGAGTTTACTTA\r\n", "gi|318053986|gb|FQ662476.1|FQ662476\tFQ662476 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF04FM1, mRNA sequence\tGATCATACATCAAACTGAAGAACATTCATGAAAATCTAACAAGATTGAAAAACACAAAGTTAGAGATTTGTATTAAAACTAAAATATTAGACGAGGTAAAAAAGCTAATTGAATTGCCTTGTCTTGCTGATGTGTCTGCGGATGATATTGTAGATCAAGTTTCTTTAAATATGGAGAATATTGACTATACACGTGCGAAAGGGAATAAAATTTCTGAATTTACAATAGCAGGAACTCGTATAATGGGTGTGAGTTTTTTTGGGTAATGGTAATCTGTTCTTAGCCGACCATAGAGGGAAAAGATGCATCCTTTGTGACACAAATGGAGTTATTTTACAGGAAGCAAAAATACTGGGATCGCCTTGGGGCGTATGTACAAGCGGGATGGATATTCTCATGACGCTTCCAAATGAAAAGTCGATTTTAAAATTTGACTCAACTTCATTTGAAACCATAAAAACTGTTCCTGTTGATTGTTGGTGTTACGGGATAACTGCATCTGGAAACACAATCGTCATTGGTACAGATAGATCTGTTGACATTATAACTGATGGTTTTCTTACTACAAAACGAAAAACACTTTTATCTGGCCTTGGAAATATTAGTGATGTAACAGTAGACAATGAAAATAACGTGATTTGTAGTATTTTTTCTCAACATATTGTCAGAAAACTAGA\r\n", "gi|318053985|gb|FQ662475.1|FQ662475\tFQ662475 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF05FM1, mRNA sequence\tGGAATGCATGCACTTTCAAACAGAAATTATATTTTATGTTTTATTCAACATTTAATTACTGTAATTGCAATTTTCATTTTTCTGAATAATCAAACATTTATAGTGGCCTGATACTGGTGTCATTTATCTCCAGATTATTTATTTCTGAATATACTTTCGAGATCATCTTTTTCTAGAGGTTAGAAGTACTTGATGTAAACAAACTCAAATTACCTGGTTTCAATATTCTAGCTTGAGGATGTGAAATCTAAATGCTTTAGTTTGCAGGCTGCATCATTTGTTCAGTGACTATAGTGAATAGTTTAGAAATTCTTTTTTAGATATGCATGTAGTATTGTATATATTAGTATAAAAAGCATTCATACTTGTTATTTAATTCTGTGATTAAAAAAGAGTTTCTGTGAACAGTATTAGCTTTTATTAATACTGCATTTTTTATTAAAACTACATGCATATTTTTGCTACCTACATGTATTTGTGTTGAATAACGAAATATAACTGTGCAATAAAATCCATGCAAGCATTCAGAATGACAAAACCATATGAAACCAGTGGATATGGAATCAGCAATGGTGTTAACTGATTATTTATTTTCTGAGCTTAATACATCAGCCGATCTTTTCTTTAAAAAAAAATACCAAAACAATAAAATGGACCAATTGTATAGAAAACCAGATACTTTTATTAACATAACATGCGTCTGTTAACAACTTTTTGGGGTGCCATTGGTTGAATATTGTTTGATTATGAATGATGCACTCTATAGTCACGATTATTTATACTATAAAAATAATGC\r\n", "gi|318053984|gb|FQ662474.1|FQ662474\tFQ662474 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF06FM1, mRNA sequence\tGTGAGAGTTCATTGTCGAAAGATGTCTGGTTTTCTTCATCGAGATTCGGTAGTGAATGCAAGTGTAGTAAAGTCGAACATTTTGTTCATGGAAAATGTTTTTCTGATTATTGATACACATAGAGTACATTGATACATGTATATTTGACTTTTTATCTTACACTAAAAGTCAAATCTTGTCAGACGTTTAGTACGTATTTTTAAAAATCCCCAGCTTACATTTGCGTGGAATTCGCTTACTTACAACATACATTTAAAAGCGAGAGTAATACCTAGAAATTTTGTTAACAATAACATGTAAATGATTAGCCTTAAGAAAATCACATATTTGTTTAATATGAATTTCAAATCTAAACAAAACGACCATCAAAATACATGTACATCATGTATGCTTGTAGGGAATTGATTATATCATTATATTTTCACCTAATCAGACTTCGGGCGTCGAAGTAGACGACAACTGCATCCAGTCGTACATTAAACTCCAGCTTCAGCACTCATCTCAATTCATCATCTACCGGCTGTCGGACGACAAAAAACGCATCATTGTCGATAAAATTGGACCAGTTGGGTGTACCTATGACAATTTTGTGCCAGAGCTTCAGAATGCTGGATCTAAGGGAGAGGGTCGGTACGGGGTGTTCGATTTCAATTACACCGTCAAAGAAAGAATAGTAAACAAAATCGTGTTCTTTCTATGGATTCCAGATACAATACAAGTGAAGCAGCGGATGTTATACAGTAGTAGTGTGCGCGCATTANAAACGAGACTTCCCGGAATTCACATAGAAATGCAGTGTAATGACGATTCCG\r\n", "gi|318053983|gb|FQ662473.1|FQ662473\tFQ662473 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF07FM1, mRNA sequence\tGATTCTTGATTTTCTGTATGTTATTCAAATTGGAGGCATCCTTTGTGTGAAATTTGGGATAAATGATTTTGATATATGTAGATCAGTTTCTGTAGTTTGATGACATGTTGAGTGATGTGTAGTATGTGCTGATACATTTCCATTCAGATTTAAATTCTAGCACCCACTACAAGCAATTTCAGGGATAACTTATGAAACATTCCACAAACGTTTTGTGTTACTGATTTTTTTGTGTTCATTTCACGGAAGTTAAATACAAATGAAGAGACTGAATTCACATGAAATGATTCCAATTGTATATATGTCATGTTGTGAATGCTAAACTGTATGTAGTTGGGGAAGGGAGAGGGCATGGAGCCTATTGGATAATTTGTAAATACATTTCTACATTCCATTTTCGTGTACAGAGTGGCGTGTACCTGTATATATGTGTACCTGTATATATGATTACTTACTGTTTTTATACCAATGTTCTGTGAGGAATGATTTTGTCTCGTTTGATGAATTGACAATCCACTCTTTGTTTGGAGAACTTTATCAGATGCACCCCACCGCACGTGTTTCTGCACGGTTTTTGTGAATTTTGAAGACAGTGCAAAATCAACACCCTAGTCTCTTGTCAGATCTGTTATTTTAGTCAAAATATATTTATTTATTAATTTGTTACGATTTTTTGCTATGTTTTTATTGTGTATATTATTTGTACAAGTGTTGAAGTGACAATTTTCTGATCGTTGTTGGGATTACA\r\n", "gi|318053982|gb|FQ662472.1|FQ662472\tFQ662472 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF08FM1, mRNA sequence\tGGAGAACGAGAGATGTAGAGACCATGGATGAAGCGCTAACTCCACTCTAGAACCTTGTGAGATCATCAGTAGAAAGAGACATTCTAATCCGGACCAGAACTTTAGCCACAGCCATTAACCGTAGAATTAGTGTGGAGTTGAATTCTTGTTCCGATTTTAGAAGGTTTTCTTTATTCTGGGTCTTCTTTGTTTCTGTGATTCAAGCCTTTGACTGTTTTTGGAGGAGATAAAAAGGAAACTGTCCTTGAGGATTTTGCCGACGATTGTTCTCAGTAGACACTTACCGCTGTCTTGATCCCTTATGACTTTTTGGAATTTGAATGTTTGACCTAACGAAATGTCTGTGATAAAACGAGATCTATACACATCCAGAAATCCAATCTATACAGCATTATATTTTATTCTGACTGTTCAGTTCTATGGAGTATTAATTTTTGCGGGACATGTAAACGAAAAAGAACAAACATACACATTAAATATACCGTGGCACATAGGAAACCTTCACCCACGACATGTGCAATACACAGTTCACGGAATTCCAGAAATCCAAACCCTCCGACTCAAACGGAACGACAACATTAATATCAACGTGCCCTCCTGTATCATAGATCAGGGTTTTACTATTTGTGAATACGGAAATATACAAGATATTGCCTTCTATCACACTACCGATAAACAAGGGGCGTTTGCAATCACACTGGACCGCACGGCACCAACGGACACACAGACACAACTTGAAGGCGTTTTGGTCTCCGGAAAAGACGCGTTTGTGTTGGAGCCAAATGGTCCCCTGGGACACAGCCTGACCCCCGCCCAC\r\n", "gi|318053981|gb|FQ662471.1|FQ662471\tFQ662471 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF09FM1, mRNA sequence\tGGGAAATGGTGAAAATGGTGGGTGGGCGAGCTGCCAAAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTATCAAGATGGAGGAGATTAAAAAGTTTGCCATAGCTCCAGAAAAGATCCAAGAAGCATTGTATCCTCCCTGTATGAAGGTTTCTGATCTGACTGAGGAAAAGTTGATTACTATAGCTATACGTACAAGATTGTCAGTGCAGGGATATGTGCAATTGGTTAGTAAAATCTATGATGAAGACAGATGTCCAAAAAGAACTCTGATTCTGAAGGAGACAATGGAAGGCAGGCGACCAGCAACCATGTTCGTAAGATTATGGAGGGAGAAGACAGAGATAAATCCTAAAGTGGGATCCTGGTTCAAGTTCTGTCGCTGAAGCTTACTGACTACAAGGACAGCAGAGAAATCCACTCCACCCCCTCCACAGTGCTACGAGAGGTGTCGGAGGAGCAGCCCCCCACACAGACAGACACACAGGCAGCCAGTCAATAAACTCGCACCAAGTACCCGTTAATCTCATTTTCCTCACAGCGGTATAAAGAAGATGTAGACATTTTTTTCCCACTTCATTAATGGTAGCCCTATTTCCACAATTGATTGCTATTGAATTTATAGTAGTCGATCTCTGTAGATTCCTGTCAATGCTTTTGTCTGTCTGTAAGTAGAGGATGCACAGTGCACGTAACCTTAAACCAGTTCTCTAGTTCAAAGGTCAAGATTGAAAGACCTGACAGTAAAACATATACCAATGACTGACTGTGTATCTCTGAAAAAGGTGTGCAATGTACTGTACTTTAACCAA\r\n", "gi|318053980|gb|FQ662470.1|FQ662470\tFQ662470 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF10FM1, mRNA sequence\tGAATCGAGAGGAGATCATCATGTGTATTGTTTTCATTTCCATTTTCACTCTCATCGGTAGAATCATGTAAGAGAAGAGCACGGGTATCTGACAATGTATCTGTTTTAAAATTTTTATAACAATATAATCAATACATTTGATATGTAAGTTAATGCTAGCTGTATTTCTTTCTGTGCTTGGCATGTTGTTCTTAAATACATGAAACATCTACATGTTTTCTTCAATAACTAGCATGAACATATGATAAATATGATAAAAGTGAGTTGGCTGTATGTTTAAAAAATTCCACATCTGTGCGAGTTTTAAAAACTGAAATATTGCTGATTTTTTTTAATGTGATTTCTCATCTTGTAATATAAATATATGGGATGACTGACTTGTAGACCCCTAAAAATGTATATTTTTTAACTTTATTGATTCATAATTGGTAAAATTTTATTCACGAAACTTTTCTACTTGTTAAATTGTATAGAGCTTTTATGTGTACATGTATTACTTTACCTTAATATATTGAGTATTTATATATGCTTAGGTATATACCTAGTCACTGTTATATCTCTGTAGTCCAGAGACTAAGTGTGAAACATACAATGGCTGTGGAGAGTTGTTTTCAAATAATCATAACTGATGCTCATTTTGCTATCTTCTTTCATTGAGTTATCTTTCTTGGTTGTTCATAGTTCTAACGGTTGTGACTATCTTTACATTCCATGCCATGCAATTACATGAATGTGTTCAGAATAAGATTTACAAAATCATTATTAATTTCATATACCAATGTACGTGTATTTTATATGCATTACAACATTTTGAAATCGTTTA\r\n", "gi|318053979|gb|FQ662469.1|FQ662469\tFQ662469 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF11FM1, mRNA sequence\tGATCATATATGGATGATATCTAACATATAGCTGACTTCATTCTTTTTCATTTATTAAATTTGCCCCGTATTACAATCCTTTGGGAGAAGGGGAGACATGTGTTTTTTTGTATAAAAAAACAATACCCACTAGTTTAGAGAGTTCTTGTAGAAAATAATCTGTTGTTGCTACAGATATACCAGATAGTTATTATATTCAGACAGAATGCAACGATTTAGAGTATAACATGTTAAACAATGAAATGCAGTATTCATGTATCAAAATCCAGTAGACAATCTTGAAAACAAGAGCTCATAACTCACCAGACAAAACACAAAGTATTTTTTATGTGCTAGCATTAGAGATACCATATTTTGATATTAAGATTTTTGTGTCATATTTTATGTATGTTCAGTGTGCTTACGGACCAAACAGAGGTTGTGATTGCAAGGTTATTGTAGTGTTATCATAGAGTTGTGAGAGTTATAGAAAGCTAGCTGGTATAGTTTTATACATTCTCTAGAGAACAGTATTTGTTGTTTGTTGTCAATGTTTGAAATACTGTACAAATGTTTGTTAAGTCCATTAACTCTTGCCAAACTAGCAAGTCCCAGCTTACAAAGTGCAATTAGTGGTGTTTTGGTTTGTGTTTTTGTTCCTATCAATCCTGATTCACGGTTTTAAAGAATGTGTGATCATTCATAACAATGTAGAGCTTGCCATGTTTAATGTTCAAATCCAAGGCTTGACTGTTATGCTATGTGTACAATAAATGGGGCCTCAAAA\r\n", "gi|318053978|gb|FQ662468.1|FQ662468\tFQ662468 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF12FM1, mRNA sequence\tGGAAGGGAAACCCCTTCCTTCTGTGGATTTGGGAAAGAAAAATCCTGCCTCCGATTTCAGCAGTTAATGTAAAACGAGAGTGAACTTCAACATTATGGCTGCGGATTTCGAATATAAACAGATGTTATTAGAACTGGATAAGTCTCTGAAAGCCGAAGAATTTGAATCCTTAAAATTTTTATGCAAAGATGAGGTGAAAAAACGAGAAAGAGAAAGTGTCAACCGACCTACAGATTTATGGGAAATTTTGGAGACGAGGGAGAAACTGGGTCCAAATAATCTAGCCTTCTTAAAACAGATAATTAAAGGTTCCTGTAATGGCCGTCGTGATGTTTTGAGAGTTATTGAGAACTTTGAGAGGGGAATTCCACCTGATAGTCAACGACCTGTGAATTCATCATCATCAGTCCCCACGAATCAGCCGTACGTGCAGCAGCCAGTGTTTTATAACCCAGTTCTCAAACAGTATGGGCAACAACCAGGTATGCCTACTCGTGATCATCCCCTGGGTACTTCCATCATCCACTCCAGTGCAGTGAATGTGGACAAATACATGAAAGAAATCAATTTCCTAACGAAGAATTTGGGGAGGGAGTGGAGGTTTTTCATGAGGACCCTTGGAGTGACGGATGGTGATATGATGTCTGTGGAGCAGGACCACCCCCGCAGTTTGAGGGACCAGATTTACCAGTGCCTGGTCCTGTGGATCAGTAACAATGGTGGACAGTTTGACAGGGGCAGAGTAGTTGCGGCACTGCGGGATTCTGCGGTGGAGAGATATGATTTAGCCGGAAGGATTCAAGACTGTG\r\n" ] } ], "prompt_number": 59 }, { "cell_type": "code", "collapsed": false, "input": [ "#Translate pipes to tab so SPID is in separate column for Joining\n", "!tr '|' \"\\t\" /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 60 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "gi\t318053987\tgb\tFQ662477.1\tFQ662477\tFQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence\tGGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTACAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTTATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAGATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACAATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCCTACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATAAAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGATTAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATTATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTTTATGATCGAAAATGTTTTATTTCCTTTATTATTTATCTGGATATATTATCTGACTCTATACACAAAAGAAGCAAAGCTTTGATGCGTAGTACACATGTGCTGTCAGCCTCATTTTGGTGATGACAATCCAGTTCCTGGTCATCGGTGTGTTTGAAAGCTGCATTCTCCTCAATGTTGTTGGTTTAGCTTCAAGCAAGAGTTTACTTA\r\n", "gi\t318053986\tgb\tFQ662476.1\tFQ662476\tFQ662476 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF04FM1, mRNA sequence\tGATCATACATCAAACTGAAGAACATTCATGAAAATCTAACAAGATTGAAAAACACAAAGTTAGAGATTTGTATTAAAACTAAAATATTAGACGAGGTAAAAAAGCTAATTGAATTGCCTTGTCTTGCTGATGTGTCTGCGGATGATATTGTAGATCAAGTTTCTTTAAATATGGAGAATATTGACTATACACGTGCGAAAGGGAATAAAATTTCTGAATTTACAATAGCAGGAACTCGTATAATGGGTGTGAGTTTTTTTGGGTAATGGTAATCTGTTCTTAGCCGACCATAGAGGGAAAAGATGCATCCTTTGTGACACAAATGGAGTTATTTTACAGGAAGCAAAAATACTGGGATCGCCTTGGGGCGTATGTACAAGCGGGATGGATATTCTCATGACGCTTCCAAATGAAAAGTCGATTTTAAAATTTGACTCAACTTCATTTGAAACCATAAAAACTGTTCCTGTTGATTGTTGGTGTTACGGGATAACTGCATCTGGAAACACAATCGTCATTGGTACAGATAGATCTGTTGACATTATAACTGATGGTTTTCTTACTACAAAACGAAAAACACTTTTATCTGGCCTTGGAAATATTAGTGATGTAACAGTAGACAATGAAAATAACGTGATTTGTAGTATTTTTTCTCAACATATTGTCAGAAAACTAGA\r\n", "gi\t318053985\tgb\tFQ662475.1\tFQ662475\tFQ662475 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF05FM1, mRNA sequence\tGGAATGCATGCACTTTCAAACAGAAATTATATTTTATGTTTTATTCAACATTTAATTACTGTAATTGCAATTTTCATTTTTCTGAATAATCAAACATTTATAGTGGCCTGATACTGGTGTCATTTATCTCCAGATTATTTATTTCTGAATATACTTTCGAGATCATCTTTTTCTAGAGGTTAGAAGTACTTGATGTAAACAAACTCAAATTACCTGGTTTCAATATTCTAGCTTGAGGATGTGAAATCTAAATGCTTTAGTTTGCAGGCTGCATCATTTGTTCAGTGACTATAGTGAATAGTTTAGAAATTCTTTTTTAGATATGCATGTAGTATTGTATATATTAGTATAAAAAGCATTCATACTTGTTATTTAATTCTGTGATTAAAAAAGAGTTTCTGTGAACAGTATTAGCTTTTATTAATACTGCATTTTTTATTAAAACTACATGCATATTTTTGCTACCTACATGTATTTGTGTTGAATAACGAAATATAACTGTGCAATAAAATCCATGCAAGCATTCAGAATGACAAAACCATATGAAACCAGTGGATATGGAATCAGCAATGGTGTTAACTGATTATTTATTTTCTGAGCTTAATACATCAGCCGATCTTTTCTTTAAAAAAAAATACCAAAACAATAAAATGGACCAATTGTATAGAAAACCAGATACTTTTATTAACATAACATGCGTCTGTTAACAACTTTTTGGGGTGCCATTGGTTGAATATTGTTTGATTATGAATGATGCACTCTATAGTCACGATTATTTATACTATAAAAATAATGC\r\n", "gi\t318053984\tgb\tFQ662474.1\tFQ662474\tFQ662474 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF06FM1, mRNA sequence\tGTGAGAGTTCATTGTCGAAAGATGTCTGGTTTTCTTCATCGAGATTCGGTAGTGAATGCAAGTGTAGTAAAGTCGAACATTTTGTTCATGGAAAATGTTTTTCTGATTATTGATACACATAGAGTACATTGATACATGTATATTTGACTTTTTATCTTACACTAAAAGTCAAATCTTGTCAGACGTTTAGTACGTATTTTTAAAAATCCCCAGCTTACATTTGCGTGGAATTCGCTTACTTACAACATACATTTAAAAGCGAGAGTAATACCTAGAAATTTTGTTAACAATAACATGTAAATGATTAGCCTTAAGAAAATCACATATTTGTTTAATATGAATTTCAAATCTAAACAAAACGACCATCAAAATACATGTACATCATGTATGCTTGTAGGGAATTGATTATATCATTATATTTTCACCTAATCAGACTTCGGGCGTCGAAGTAGACGACAACTGCATCCAGTCGTACATTAAACTCCAGCTTCAGCACTCATCTCAATTCATCATCTACCGGCTGTCGGACGACAAAAAACGCATCATTGTCGATAAAATTGGACCAGTTGGGTGTACCTATGACAATTTTGTGCCAGAGCTTCAGAATGCTGGATCTAAGGGAGAGGGTCGGTACGGGGTGTTCGATTTCAATTACACCGTCAAAGAAAGAATAGTAAACAAAATCGTGTTCTTTCTATGGATTCCAGATACAATACAAGTGAAGCAGCGGATGTTATACAGTAGTAGTGTGCGCGCATTANAAACGAGACTTCCCGGAATTCACATAGAAATGCAGTGTAATGACGATTCCG\r\n", "gi\t318053983\tgb\tFQ662473.1\tFQ662473\tFQ662473 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF07FM1, mRNA sequence\tGATTCTTGATTTTCTGTATGTTATTCAAATTGGAGGCATCCTTTGTGTGAAATTTGGGATAAATGATTTTGATATATGTAGATCAGTTTCTGTAGTTTGATGACATGTTGAGTGATGTGTAGTATGTGCTGATACATTTCCATTCAGATTTAAATTCTAGCACCCACTACAAGCAATTTCAGGGATAACTTATGAAACATTCCACAAACGTTTTGTGTTACTGATTTTTTTGTGTTCATTTCACGGAAGTTAAATACAAATGAAGAGACTGAATTCACATGAAATGATTCCAATTGTATATATGTCATGTTGTGAATGCTAAACTGTATGTAGTTGGGGAAGGGAGAGGGCATGGAGCCTATTGGATAATTTGTAAATACATTTCTACATTCCATTTTCGTGTACAGAGTGGCGTGTACCTGTATATATGTGTACCTGTATATATGATTACTTACTGTTTTTATACCAATGTTCTGTGAGGAATGATTTTGTCTCGTTTGATGAATTGACAATCCACTCTTTGTTTGGAGAACTTTATCAGATGCACCCCACCGCACGTGTTTCTGCACGGTTTTTGTGAATTTTGAAGACAGTGCAAAATCAACACCCTAGTCTCTTGTCAGATCTGTTATTTTAGTCAAAATATATTTATTTATTAATTTGTTACGATTTTTTGCTATGTTTTTATTGTGTATATTATTTGTACAAGTGTTGAAGTGACAATTTTCTGATCGTTGTTGGGATTACA\r\n", "gi\t318053982\tgb\tFQ662472.1\tFQ662472\tFQ662472 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF08FM1, mRNA sequence\tGGAGAACGAGAGATGTAGAGACCATGGATGAAGCGCTAACTCCACTCTAGAACCTTGTGAGATCATCAGTAGAAAGAGACATTCTAATCCGGACCAGAACTTTAGCCACAGCCATTAACCGTAGAATTAGTGTGGAGTTGAATTCTTGTTCCGATTTTAGAAGGTTTTCTTTATTCTGGGTCTTCTTTGTTTCTGTGATTCAAGCCTTTGACTGTTTTTGGAGGAGATAAAAAGGAAACTGTCCTTGAGGATTTTGCCGACGATTGTTCTCAGTAGACACTTACCGCTGTCTTGATCCCTTATGACTTTTTGGAATTTGAATGTTTGACCTAACGAAATGTCTGTGATAAAACGAGATCTATACACATCCAGAAATCCAATCTATACAGCATTATATTTTATTCTGACTGTTCAGTTCTATGGAGTATTAATTTTTGCGGGACATGTAAACGAAAAAGAACAAACATACACATTAAATATACCGTGGCACATAGGAAACCTTCACCCACGACATGTGCAATACACAGTTCACGGAATTCCAGAAATCCAAACCCTCCGACTCAAACGGAACGACAACATTAATATCAACGTGCCCTCCTGTATCATAGATCAGGGTTTTACTATTTGTGAATACGGAAATATACAAGATATTGCCTTCTATCACACTACCGATAAACAAGGGGCGTTTGCAATCACACTGGACCGCACGGCACCAACGGACACACAGACACAACTTGAAGGCGTTTTGGTCTCCGGAAAAGACGCGTTTGTGTTGGAGCCAAATGGTCCCCTGGGACACAGCCTGACCCCCGCCCAC\r\n", "gi\t318053981\tgb\tFQ662471.1\tFQ662471\tFQ662471 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF09FM1, mRNA sequence\tGGGAAATGGTGAAAATGGTGGGTGGGCGAGCTGCCAAAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTATCAAGATGGAGGAGATTAAAAAGTTTGCCATAGCTCCAGAAAAGATCCAAGAAGCATTGTATCCTCCCTGTATGAAGGTTTCTGATCTGACTGAGGAAAAGTTGATTACTATAGCTATACGTACAAGATTGTCAGTGCAGGGATATGTGCAATTGGTTAGTAAAATCTATGATGAAGACAGATGTCCAAAAAGAACTCTGATTCTGAAGGAGACAATGGAAGGCAGGCGACCAGCAACCATGTTCGTAAGATTATGGAGGGAGAAGACAGAGATAAATCCTAAAGTGGGATCCTGGTTCAAGTTCTGTCGCTGAAGCTTACTGACTACAAGGACAGCAGAGAAATCCACTCCACCCCCTCCACAGTGCTACGAGAGGTGTCGGAGGAGCAGCCCCCCACACAGACAGACACACAGGCAGCCAGTCAATAAACTCGCACCAAGTACCCGTTAATCTCATTTTCCTCACAGCGGTATAAAGAAGATGTAGACATTTTTTTCCCACTTCATTAATGGTAGCCCTATTTCCACAATTGATTGCTATTGAATTTATAGTAGTCGATCTCTGTAGATTCCTGTCAATGCTTTTGTCTGTCTGTAAGTAGAGGATGCACAGTGCACGTAACCTTAAACCAGTTCTCTAGTTCAAAGGTCAAGATTGAAAGACCTGACAGTAAAACATATACCAATGACTGACTGTGTATCTCTGAAAAAGGTGTGCAATGTACTGTACTTTAACCAA\r\n", "gi\t318053980\tgb\tFQ662470.1\tFQ662470\tFQ662470 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF10FM1, mRNA sequence\tGAATCGAGAGGAGATCATCATGTGTATTGTTTTCATTTCCATTTTCACTCTCATCGGTAGAATCATGTAAGAGAAGAGCACGGGTATCTGACAATGTATCTGTTTTAAAATTTTTATAACAATATAATCAATACATTTGATATGTAAGTTAATGCTAGCTGTATTTCTTTCTGTGCTTGGCATGTTGTTCTTAAATACATGAAACATCTACATGTTTTCTTCAATAACTAGCATGAACATATGATAAATATGATAAAAGTGAGTTGGCTGTATGTTTAAAAAATTCCACATCTGTGCGAGTTTTAAAAACTGAAATATTGCTGATTTTTTTTAATGTGATTTCTCATCTTGTAATATAAATATATGGGATGACTGACTTGTAGACCCCTAAAAATGTATATTTTTTAACTTTATTGATTCATAATTGGTAAAATTTTATTCACGAAACTTTTCTACTTGTTAAATTGTATAGAGCTTTTATGTGTACATGTATTACTTTACCTTAATATATTGAGTATTTATATATGCTTAGGTATATACCTAGTCACTGTTATATCTCTGTAGTCCAGAGACTAAGTGTGAAACATACAATGGCTGTGGAGAGTTGTTTTCAAATAATCATAACTGATGCTCATTTTGCTATCTTCTTTCATTGAGTTATCTTTCTTGGTTGTTCATAGTTCTAACGGTTGTGACTATCTTTACATTCCATGCCATGCAATTACATGAATGTGTTCAGAATAAGATTTACAAAATCATTATTAATTTCATATACCAATGTACGTGTATTTTATATGCATTACAACATTTTGAAATCGTTTA\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "gi\t318053979\tgb\tFQ662469.1\tFQ662469\tFQ662469 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF11FM1, mRNA sequence\tGATCATATATGGATGATATCTAACATATAGCTGACTTCATTCTTTTTCATTTATTAAATTTGCCCCGTATTACAATCCTTTGGGAGAAGGGGAGACATGTGTTTTTTTGTATAAAAAAACAATACCCACTAGTTTAGAGAGTTCTTGTAGAAAATAATCTGTTGTTGCTACAGATATACCAGATAGTTATTATATTCAGACAGAATGCAACGATTTAGAGTATAACATGTTAAACAATGAAATGCAGTATTCATGTATCAAAATCCAGTAGACAATCTTGAAAACAAGAGCTCATAACTCACCAGACAAAACACAAAGTATTTTTTATGTGCTAGCATTAGAGATACCATATTTTGATATTAAGATTTTTGTGTCATATTTTATGTATGTTCAGTGTGCTTACGGACCAAACAGAGGTTGTGATTGCAAGGTTATTGTAGTGTTATCATAGAGTTGTGAGAGTTATAGAAAGCTAGCTGGTATAGTTTTATACATTCTCTAGAGAACAGTATTTGTTGTTTGTTGTCAATGTTTGAAATACTGTACAAATGTTTGTTAAGTCCATTAACTCTTGCCAAACTAGCAAGTCCCAGCTTACAAAGTGCAATTAGTGGTGTTTTGGTTTGTGTTTTTGTTCCTATCAATCCTGATTCACGGTTTTAAAGAATGTGTGATCATTCATAACAATGTAGAGCTTGCCATGTTTAATGTTCAAATCCAAGGCTTGACTGTTATGCTATGTGTACAATAAATGGGGCCTCAAAA\r\n", "gi\t318053978\tgb\tFQ662468.1\tFQ662468\tFQ662468 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF12FM1, mRNA sequence\tGGAAGGGAAACCCCTTCCTTCTGTGGATTTGGGAAAGAAAAATCCTGCCTCCGATTTCAGCAGTTAATGTAAAACGAGAGTGAACTTCAACATTATGGCTGCGGATTTCGAATATAAACAGATGTTATTAGAACTGGATAAGTCTCTGAAAGCCGAAGAATTTGAATCCTTAAAATTTTTATGCAAAGATGAGGTGAAAAAACGAGAAAGAGAAAGTGTCAACCGACCTACAGATTTATGGGAAATTTTGGAGACGAGGGAGAAACTGGGTCCAAATAATCTAGCCTTCTTAAAACAGATAATTAAAGGTTCCTGTAATGGCCGTCGTGATGTTTTGAGAGTTATTGAGAACTTTGAGAGGGGAATTCCACCTGATAGTCAACGACCTGTGAATTCATCATCATCAGTCCCCACGAATCAGCCGTACGTGCAGCAGCCAGTGTTTTATAACCCAGTTCTCAAACAGTATGGGCAACAACCAGGTATGCCTACTCGTGATCATCCCCTGGGTACTTCCATCATCCACTCCAGTGCAGTGAATGTGGACAAATACATGAAAGAAATCAATTTCCTAACGAAGAATTTGGGGAGGGAGTGGAGGTTTTTCATGAGGACCCTTGGAGTGACGGATGGTGATATGATGTCTGTGGAGCAGGACCACCCCCGCAGTTTGAGGGACCAGATTTACCAGTGCCTGGTCCTGTGGATCAGTAACAATGGTGGACAGTTTGACAGGGGCAGAGTAGTTGCGGCACTGCGGGATTCTGCGGTGGAGAGATATGATTTAGCCGGAAGGATTCAAGACTGTG\r\n" ] } ], "prompt_number": 61 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "gi\t318053987\tgb\tFQ662477.1\tFQ662477\tFQ662477 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF03FM1, mRNA sequence\tGGACTTCCGCCATTTTGCATTTTGACATGTAAACATTCACAGTAAATATGTCTAGGGATTCGAATAATTACAGTCAAAGCTACAGGCTTGTTGTCGTCGGTGGTGGCGGCGTAGGAAAAAGTGCACTCACAATCCAATTTATACAGTCATATTTTGTAACAGACTATGATCCAACAATAGAAGATTCCTATACCAAACAGTGCGTCATAGATGAAGTGGTCGCAAGACTAGACATTTTAGACACAGCCGGACAAGAAGAGTTCTGCGCCATGAGGGAACAATATATGAGATCAGGGGAGGGGTTCCTACTGGTGTACTCTGTTACAGACAGGGCAAGTTTCAACGAAGCCTACAAATTCCACAAACAGATTCTCCGTGTAAAAGACCGGGAGGAGTTCCCCATGATACTGGTGGCGAATAAAGCGGACCTGGAACACTCGAGGATGGTTACAAGAGAGGAGGGACAAGAACTCTCAGCCCAGTTGAAGATTAGTTATATTGAAGCAAGTGCCAAAGTCAGGATGAATGTAGACAAAGCTTTCTATGATCTGGTTAGAATTATTAGGCGGTTTCAAGCTAATGAAAGTCCACCGGTCAAAGCGCCTAAACGAAGTAAAAAATGCACAATTTTATGATCGAAAATGTTTTATTTCCTTTATTATTTATCTGGATATATTATCTGACTCTATACACAAAAGAAGCAAAGCTTTGATGCGTAGTACACATGTGCTGTCAGCCTCATTTTGGTGATGACAATCCAGTTCCTGGTCATCGGTGTGTTTGAAAGCTGCATTCTCCTCAATGTTGTTGGTTTAGCTTCAAGCAAGAGTTTACTTA\r\n", "gi\t318053986\tgb\tFQ662476.1\tFQ662476\tFQ662476 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF04FM1, mRNA sequence\tGATCATACATCAAACTGAAGAACATTCATGAAAATCTAACAAGATTGAAAAACACAAAGTTAGAGATTTGTATTAAAACTAAAATATTAGACGAGGTAAAAAAGCTAATTGAATTGCCTTGTCTTGCTGATGTGTCTGCGGATGATATTGTAGATCAAGTTTCTTTAAATATGGAGAATATTGACTATACACGTGCGAAAGGGAATAAAATTTCTGAATTTACAATAGCAGGAACTCGTATAATGGGTGTGAGTTTTTTTGGGTAATGGTAATCTGTTCTTAGCCGACCATAGAGGGAAAAGATGCATCCTTTGTGACACAAATGGAGTTATTTTACAGGAAGCAAAAATACTGGGATCGCCTTGGGGCGTATGTACAAGCGGGATGGATATTCTCATGACGCTTCCAAATGAAAAGTCGATTTTAAAATTTGACTCAACTTCATTTGAAACCATAAAAACTGTTCCTGTTGATTGTTGGTGTTACGGGATAACTGCATCTGGAAACACAATCGTCATTGGTACAGATAGATCTGTTGACATTATAACTGATGGTTTTCTTACTACAAAACGAAAAACACTTTTATCTGGCCTTGGAAATATTAGTGATGTAACAGTAGACAATGAAAATAACGTGATTTGTAGTATTTTTTCTCAACATATTGTCAGAAAACTAGA\r\n", "gi\t318053985\tgb\tFQ662475.1\tFQ662475\tFQ662475 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF05FM1, mRNA sequence\tGGAATGCATGCACTTTCAAACAGAAATTATATTTTATGTTTTATTCAACATTTAATTACTGTAATTGCAATTTTCATTTTTCTGAATAATCAAACATTTATAGTGGCCTGATACTGGTGTCATTTATCTCCAGATTATTTATTTCTGAATATACTTTCGAGATCATCTTTTTCTAGAGGTTAGAAGTACTTGATGTAAACAAACTCAAATTACCTGGTTTCAATATTCTAGCTTGAGGATGTGAAATCTAAATGCTTTAGTTTGCAGGCTGCATCATTTGTTCAGTGACTATAGTGAATAGTTTAGAAATTCTTTTTTAGATATGCATGTAGTATTGTATATATTAGTATAAAAAGCATTCATACTTGTTATTTAATTCTGTGATTAAAAAAGAGTTTCTGTGAACAGTATTAGCTTTTATTAATACTGCATTTTTTATTAAAACTACATGCATATTTTTGCTACCTACATGTATTTGTGTTGAATAACGAAATATAACTGTGCAATAAAATCCATGCAAGCATTCAGAATGACAAAACCATATGAAACCAGTGGATATGGAATCAGCAATGGTGTTAACTGATTATTTATTTTCTGAGCTTAATACATCAGCCGATCTTTTCTTTAAAAAAAAATACCAAAACAATAAAATGGACCAATTGTATAGAAAACCAGATACTTTTATTAACATAACATGCGTCTGTTAACAACTTTTTGGGGTGCCATTGGTTGAATATTGTTTGATTATGAATGATGCACTCTATAGTCACGATTATTTATACTATAAAAATAATGC\r\n", "gi\t318053984\tgb\tFQ662474.1\tFQ662474\tFQ662474 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF06FM1, mRNA sequence\tGTGAGAGTTCATTGTCGAAAGATGTCTGGTTTTCTTCATCGAGATTCGGTAGTGAATGCAAGTGTAGTAAAGTCGAACATTTTGTTCATGGAAAATGTTTTTCTGATTATTGATACACATAGAGTACATTGATACATGTATATTTGACTTTTTATCTTACACTAAAAGTCAAATCTTGTCAGACGTTTAGTACGTATTTTTAAAAATCCCCAGCTTACATTTGCGTGGAATTCGCTTACTTACAACATACATTTAAAAGCGAGAGTAATACCTAGAAATTTTGTTAACAATAACATGTAAATGATTAGCCTTAAGAAAATCACATATTTGTTTAATATGAATTTCAAATCTAAACAAAACGACCATCAAAATACATGTACATCATGTATGCTTGTAGGGAATTGATTATATCATTATATTTTCACCTAATCAGACTTCGGGCGTCGAAGTAGACGACAACTGCATCCAGTCGTACATTAAACTCCAGCTTCAGCACTCATCTCAATTCATCATCTACCGGCTGTCGGACGACAAAAAACGCATCATTGTCGATAAAATTGGACCAGTTGGGTGTACCTATGACAATTTTGTGCCAGAGCTTCAGAATGCTGGATCTAAGGGAGAGGGTCGGTACGGGGTGTTCGATTTCAATTACACCGTCAAAGAAAGAATAGTAAACAAAATCGTGTTCTTTCTATGGATTCCAGATACAATACAAGTGAAGCAGCGGATGTTATACAGTAGTAGTGTGCGCGCATTANAAACGAGACTTCCCGGAATTCACATAGAAATGCAGTGTAATGACGATTCCG\r\n", "gi\t318053983\tgb\tFQ662473.1\tFQ662473\tFQ662473 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF07FM1, mRNA sequence\tGATTCTTGATTTTCTGTATGTTATTCAAATTGGAGGCATCCTTTGTGTGAAATTTGGGATAAATGATTTTGATATATGTAGATCAGTTTCTGTAGTTTGATGACATGTTGAGTGATGTGTAGTATGTGCTGATACATTTCCATTCAGATTTAAATTCTAGCACCCACTACAAGCAATTTCAGGGATAACTTATGAAACATTCCACAAACGTTTTGTGTTACTGATTTTTTTGTGTTCATTTCACGGAAGTTAAATACAAATGAAGAGACTGAATTCACATGAAATGATTCCAATTGTATATATGTCATGTTGTGAATGCTAAACTGTATGTAGTTGGGGAAGGGAGAGGGCATGGAGCCTATTGGATAATTTGTAAATACATTTCTACATTCCATTTTCGTGTACAGAGTGGCGTGTACCTGTATATATGTGTACCTGTATATATGATTACTTACTGTTTTTATACCAATGTTCTGTGAGGAATGATTTTGTCTCGTTTGATGAATTGACAATCCACTCTTTGTTTGGAGAACTTTATCAGATGCACCCCACCGCACGTGTTTCTGCACGGTTTTTGTGAATTTTGAAGACAGTGCAAAATCAACACCCTAGTCTCTTGTCAGATCTGTTATTTTAGTCAAAATATATTTATTTATTAATTTGTTACGATTTTTTGCTATGTTTTTATTGTGTATATTATTTGTACAAGTGTTGAAGTGACAATTTTCTGATCGTTGTTGGGATTACA\r\n", "gi\t318053982\tgb\tFQ662472.1\tFQ662472\tFQ662472 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF08FM1, mRNA sequence\tGGAGAACGAGAGATGTAGAGACCATGGATGAAGCGCTAACTCCACTCTAGAACCTTGTGAGATCATCAGTAGAAAGAGACATTCTAATCCGGACCAGAACTTTAGCCACAGCCATTAACCGTAGAATTAGTGTGGAGTTGAATTCTTGTTCCGATTTTAGAAGGTTTTCTTTATTCTGGGTCTTCTTTGTTTCTGTGATTCAAGCCTTTGACTGTTTTTGGAGGAGATAAAAAGGAAACTGTCCTTGAGGATTTTGCCGACGATTGTTCTCAGTAGACACTTACCGCTGTCTTGATCCCTTATGACTTTTTGGAATTTGAATGTTTGACCTAACGAAATGTCTGTGATAAAACGAGATCTATACACATCCAGAAATCCAATCTATACAGCATTATATTTTATTCTGACTGTTCAGTTCTATGGAGTATTAATTTTTGCGGGACATGTAAACGAAAAAGAACAAACATACACATTAAATATACCGTGGCACATAGGAAACCTTCACCCACGACATGTGCAATACACAGTTCACGGAATTCCAGAAATCCAAACCCTCCGACTCAAACGGAACGACAACATTAATATCAACGTGCCCTCCTGTATCATAGATCAGGGTTTTACTATTTGTGAATACGGAAATATACAAGATATTGCCTTCTATCACACTACCGATAAACAAGGGGCGTTTGCAATCACACTGGACCGCACGGCACCAACGGACACACAGACACAACTTGAAGGCGTTTTGGTCTCCGGAAAAGACGCGTTTGTGTTGGAGCCAAATGGTCCCCTGGGACACAGCCTGACCCCCGCCCAC\r\n", "gi\t318053981\tgb\tFQ662471.1\tFQ662471\tFQ662471 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF09FM1, mRNA sequence\tGGGAAATGGTGAAAATGGTGGGTGGGCGAGCTGCCAAAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTATCAAGATGGAGGAGATTAAAAAGTTTGCCATAGCTCCAGAAAAGATCCAAGAAGCATTGTATCCTCCCTGTATGAAGGTTTCTGATCTGACTGAGGAAAAGTTGATTACTATAGCTATACGTACAAGATTGTCAGTGCAGGGATATGTGCAATTGGTTAGTAAAATCTATGATGAAGACAGATGTCCAAAAAGAACTCTGATTCTGAAGGAGACAATGGAAGGCAGGCGACCAGCAACCATGTTCGTAAGATTATGGAGGGAGAAGACAGAGATAAATCCTAAAGTGGGATCCTGGTTCAAGTTCTGTCGCTGAAGCTTACTGACTACAAGGACAGCAGAGAAATCCACTCCACCCCCTCCACAGTGCTACGAGAGGTGTCGGAGGAGCAGCCCCCCACACAGACAGACACACAGGCAGCCAGTCAATAAACTCGCACCAAGTACCCGTTAATCTCATTTTCCTCACAGCGGTATAAAGAAGATGTAGACATTTTTTTCCCACTTCATTAATGGTAGCCCTATTTCCACAATTGATTGCTATTGAATTTATAGTAGTCGATCTCTGTAGATTCCTGTCAATGCTTTTGTCTGTCTGTAAGTAGAGGATGCACAGTGCACGTAACCTTAAACCAGTTCTCTAGTTCAAAGGTCAAGATTGAAAGACCTGACAGTAAAACATATACCAATGACTGACTGTGTATCTCTGAAAAAGGTGTGCAATGTACTGTACTTTAACCAA\r\n", "gi\t318053980\tgb\tFQ662470.1\tFQ662470\tFQ662470 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF10FM1, mRNA sequence\tGAATCGAGAGGAGATCATCATGTGTATTGTTTTCATTTCCATTTTCACTCTCATCGGTAGAATCATGTAAGAGAAGAGCACGGGTATCTGACAATGTATCTGTTTTAAAATTTTTATAACAATATAATCAATACATTTGATATGTAAGTTAATGCTAGCTGTATTTCTTTCTGTGCTTGGCATGTTGTTCTTAAATACATGAAACATCTACATGTTTTCTTCAATAACTAGCATGAACATATGATAAATATGATAAAAGTGAGTTGGCTGTATGTTTAAAAAATTCCACATCTGTGCGAGTTTTAAAAACTGAAATATTGCTGATTTTTTTTAATGTGATTTCTCATCTTGTAATATAAATATATGGGATGACTGACTTGTAGACCCCTAAAAATGTATATTTTTTAACTTTATTGATTCATAATTGGTAAAATTTTATTCACGAAACTTTTCTACTTGTTAAATTGTATAGAGCTTTTATGTGTACATGTATTACTTTACCTTAATATATTGAGTATTTATATATGCTTAGGTATATACCTAGTCACTGTTATATCTCTGTAGTCCAGAGACTAAGTGTGAAACATACAATGGCTGTGGAGAGTTGTTTTCAAATAATCATAACTGATGCTCATTTTGCTATCTTCTTTCATTGAGTTATCTTTCTTGGTTGTTCATAGTTCTAACGGTTGTGACTATCTTTACATTCCATGCCATGCAATTACATGAATGTGTTCAGAATAAGATTTACAAAATCATTATTAATTTCATATACCAATGTACGTGTATTTTATATGCATTACAACATTTTGAAATCGTTTA\r\n", "gi\t318053979\tgb\tFQ662469.1\tFQ662469\tFQ662469 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF11FM1, mRNA sequence\tGATCATATATGGATGATATCTAACATATAGCTGACTTCATTCTTTTTCATTTATTAAATTTGCCCCGTATTACAATCCTTTGGGAGAAGGGGAGACATGTGTTTTTTTGTATAAAAAAACAATACCCACTAGTTTAGAGAGTTCTTGTAGAAAATAATCTGTTGTTGCTACAGATATACCAGATAGTTATTATATTCAGACAGAATGCAACGATTTAGAGTATAACATGTTAAACAATGAAATGCAGTATTCATGTATCAAAATCCAGTAGACAATCTTGAAAACAAGAGCTCATAACTCACCAGACAAAACACAAAGTATTTTTTATGTGCTAGCATTAGAGATACCATATTTTGATATTAAGATTTTTGTGTCATATTTTATGTATGTTCAGTGTGCTTACGGACCAAACAGAGGTTGTGATTGCAAGGTTATTGTAGTGTTATCATAGAGTTGTGAGAGTTATAGAAAGCTAGCTGGTATAGTTTTATACATTCTCTAGAGAACAGTATTTGTTGTTTGTTGTCAATGTTTGAAATACTGTACAAATGTTTGTTAAGTCCATTAACTCTTGCCAAACTAGCAAGTCCCAGCTTACAAAGTGCAATTAGTGGTGTTTTGGTTTGTGTTTTTGTTCCTATCAATCCTGATTCACGGTTTTAAAGAATGTGTGATCATTCATAACAATGTAGAGCTTGCCATGTTTAATGTTCAAATCCAAGGCTTGACTGTTATGCTATGTGTACAATAAATGGGGCCTCAAAA\r\n", "gi\t318053978\tgb\tFQ662468.1\tFQ662468\tFQ662468 Crassostrea gigas library (Genoscope - CEA) Crassostrea gigas cDNA clone WY0AAA53YF12FM1, mRNA sequence\tGGAAGGGAAACCCCTTCCTTCTGTGGATTTGGGAAAGAAAAATCCTGCCTCCGATTTCAGCAGTTAATGTAAAACGAGAGTGAACTTCAACATTATGGCTGCGGATTTCGAATATAAACAGATGTTATTAGAACTGGATAAGTCTCTGAAAGCCGAAGAATTTGAATCCTTAAAATTTTTATGCAAAGATGAGGTGAAAAAACGAGAAAGAGAAAGTGTCAACCGACCTACAGATTTATGGGAAATTTTGGAGACGAGGGAGAAACTGGGTCCAAATAATCTAGCCTTCTTAAAACAGATAATTAAAGGTTCCTGTAATGGCCGTCGTGATGTTTTGAGAGTTATTGAGAACTTTGAGAGGGGAATTCCACCTGATAGTCAACGACCTGTGAATTCATCATCATCAGTCCCCACGAATCAGCCGTACGTGCAGCAGCCAGTGTTTTATAACCCAGTTCTCAAACAGTATGGGCAACAACCAGGTATGCCTACTCGTGATCATCCCCTGGGTACTTCCATCATCCACTCCAGTGCAGTGAATGTGGACAAATACATGAAAGAAATCAATTTCCTAACGAAGAATTTGGGGAGGGAGTGGAGGTTTTTCATGAGGACCCTTGGAGTGACGGATGGTGATATGATGTCTGTGGAGCAGGACCACCCCCGCAGTTTGAGGGACCAGATTTACCAGTGCCTGGTCCTGTGGATCAGTAACAATGGTGGACAGTTTGACAGGGGCAGAGTAGTTGCGGCACTGCGGGATTCTGCGGTGGAGAGATATGATTTAGCCGGAAGGATTCAAGACTGTG\r\n" ] } ], "prompt_number": 66 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print $5,$NF}' /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_cl.tab > /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 78 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "AF280611 CGCCTGTTTATCAAAAACATCACTAGAAGATAAAGACTTTTAGCAATACCCGCCCAGTGCGAAATATTACTGTAAACGGCCGCCCTAGCGTGAGGGTGCTAAGGTAGCGAAATTCCTTGCCTTTTGATTGTGGGCCTGCATGAATGGTTTAACGAGGGTTTGACTGTCTCTAAATTTTTTATTGAAATTGTACTGAAGGTGAAGATACCTTCATTTAAAAGTTAGACAAAAAGACCCCGTGCAACTTTGAAAATTAACTTTATTCAGGAGTAAAAGATTTTTAGGTGGGGCGCCTAGAAAGCAAGTCTAACCTTTCTGAATAACTAACTCTTTCCGGATTTGACCCGATTATATTCGATCATAGGAGAAGTTACGCCGGGGATAACAGGCTAATCCTTTAGTAGAGTTCGTATTGGCTAAAGGGATTGGCACCTCGATGTTGAATCAGGGATAATAGCTTCAAGGCGTAGAGGCTTTGAAAGTAGGTCTGTTCGACCTTTAATACCCTACGTGATCTGAGTTCAGACCGG\r\n", "Crassostrea TGTAATACGCCTGAGTTGGAGACAATTTTTAAGGTAGCGCGAGTAGAAAGTTTTAAAATTTGCTTACTGCTAGGTTTGCTTCAATTTTGATATTTTTAATAACCTATTTGTAAGCCTCTATTACATGACGTAAATTTTTAGAATTGTCTTAAAGTTTAATTACATGTAGCTTATGTGTTAACCGTTATCTTTGTGAAGTGAAATACAGCTTAAGTAAAAAAAATAAAATATCTTTTCCCTATGTAATAAAAGGAGTTTTAGTGTCTTAACCTATAGCGATTCGTGCTTAGTCTAAGCTGATAGTGGCAGCCAAATTAAAATTTGGTGTTGAATGAATTGCTTGCAAGCAGGTTAAAAAATCAACTTGGTCTATTAGGGTGGTAAAGTAAAAGTATTGGGTGAAGCCTTATAAAATATTGAAAAGTACTATAAGTTAATTCTAATAAGCATACAGGGAGTGCAATAGGTTGGGTATAATAATAAATGTTTAAGTAATAAAAAATGATGAGTAGCAATAAATTGTTTGGGTATAAAAGTGATTAGCTTGGGTTAGAAGAAATCATAAAGGCTTGGGTGTAAGTTTTAAAAATAAATATGATAAGATCGAAGGTTAAGTTGAGTGCGCTTTATAAGGCACATTAGTGT\r\n", "Crassostrea CTTATCCCTTTGATGCTTCTAGTAGCAGACATGCAATTTCCTCGATTAAATGCATTTAGATTTTGAGTTTTGCCAGGGTCTCTTTATCTTATGCTTATGTCTAACATTGTAGAAAACGGAGTTGGGGCAGGGTGAACAATTTACCCTCCTTTATCAACTTACTCTTATCATGGAGTTTGTATAGACCTTGCAATTCTAAGCCTTCACCTTGCTGGTATTAGCTCTATTTTCAGGTCAATTAATTTCATAGTAACGATTAGAAATATGCGATCTGTTGGGGGCCATTTACTAGCACTATTCCCTTGATCTATTAAGGTTACTTCATTCTTGCTTTTGACTACTCTCCCAGTGTTAGCTGGAGGTCTTACTATACTTTTGACTGATCGTCATTTTAATACCTCTTTTTTTGACCCTGTCGGAGGGGGGGACCCTGTCTTATTTCAGCATTTGTTTTGATTTTTTGGTCACCCTGAGGTGTATGTCCTTATTCTTCCAGGTTTTGGAATAATTTCTCATGTCTTATGTTTTTGGTCAAGTAAAAAGACTGCATATGGAAATATGGGAATGTTTTATGCAATACTTAATATTGGGTTCTTAGGGTTTATTGTCTGGGGGCATCACATGTTTGTGGCTGGAATGGATATTGATACGCGTGCTTATTTTAGTGCTGCCACCGTTATTATTGCAGTGCCAACTGGTATTAAGGTGTTTGCATGAATTAGCACAATGCTAGGCTCTAAAGTTTCAACTCAAGCACCTATGTTGTGGTCTACTGGTTTTATTATTCTTTTTACAACAGGGGGTCTTACAGGACTTATTCTATCAAGAGCTTCAGTAGATGTGACGCTTCACGACACTTATTTTGTAACTGGTCATTTTCACTACGTCTTATCA\r\n", "AF288678 TGTAAAACGAGTCAGTCGAGTGAAAAAATTAAACGTTTCTCATATTTCAGCCAGATATAAATTGTTAACTGGATCCAGGCATTTTTCAACATCAAAACAATGGAATAAAGCACTAGTGTTAGGCGTGTATGAGAATGAATCTACAGACTCCATTGATTTTACTGGAACAGCAAGAAAATTTGATGAAAAAGCAGATGGAAAAATTTCACAGCTGTTGCTAACAGTAAAGAAGCCACTAAAATGTGGAAAAACAAGAACACTACATGCAGTAGTCCCAGAGTTTTCTTCAGTGTTAGTGACCTGCATTGGAAAAAGAGGAGAGGGATATGATGAACTGGAGACAGTGGACAAAGGGAGAGAATCCATTAGAGCTGCAGTGGCAAAAGCAGTTCTACAGTTAAGAGAGCTAGGTGAAAATGAAATTGAAGTAGACTCTTGCGGGGACACTGAAGCTTCTGCAGAGGGATGTCATCTAGCGTTGTTCTCTTATGATGACCTGAAGGCCGAGAAAAGTCGAAAGCCAGCAGTCAGGATTTCTTGTGCAACACGCTACAGCCAAGACAAAAACAGCATGGAAAAAGAATGGAGAAAGGGAGCAATTTTAGCAGAGGGCCAGAATCTCTCAAGGCGACTAATGGAAATGCCAGCTAATCTTCTTACACCCACAAAATTTGCAGAGATCGTCAAAGAACAACTGGCTGACAAGTGTGAAGTTCTGGTCAGGGATAAAGACTGGGCGGAATCAATGAAGATGGGATCATTTTTATCAGTAGCTAGAGGATCGGTAGAACCTCCTGTATTCTTGGAAATTGAGTATAAAGGGAGACAATCGGACAGCCCTCTGGCTCTAGTTGGGAAAGGAGTCACTTTTGATACTGGAGGAATCTCTATCAAGCCTTCCCAGGGCATGGATGCCATGAGGGGGGACATGGGTGGGGCTGCCTGTGTGGCGGGCAGTCTCCTAAGTGTCAGTAAACTACAGCTACCTGTTCATGTCAAAGCTTTTATACCATTATGTGAGAATATGCCAAGTGGCTCAGCAACTAAGCCTGGGGATGTAGTTACTGCAATGAATGGGAAAACAATACAGGTAGACAACACTGACGCAGAGGGACGACTTATTCTGGCTGATGCTCTGTGTTATAGTGAACAGTTCAACCCTTCCCTCATCCTAGACATGGCAACTCTAACAGGTGCAATAGATGTTGCTCTCGGGGCAGGTGCTGCTGGTGTTTTCACAAACTCAGAAAACATGTGGAACAAACTGCAAAAGGCCAGTGTAAGATCTGGGGACAGAGTGTGGAGGATGCCACTGTTCAACCATTACACAAAGAAAATAACAGAATGTCAACTAGCCGACCTTAACAACATTGGAGGGTCAAGGTCGGGTGGAGCCTGTACAGCAGCCGCCTTCCTCAAGGAATTTGTAAACAACAAAAACTGGCTTCATCTAGATATAGCTGGTGTAATGTCCAACAGTGGAGATGTAGCGTATCTAGGGAAGGGCATGTCAGGACGACCAACTAGAACTGTGATAGAATTCATCAACCTGATGAGTAAAGAAACCAAGAATTAATAAAATTATATTTCTATAGATGTCAGTTGTATTTAATTGTGTGATTCAAAGATGAACTTTGAGTTGTATCACGATATGATTGATGTTTGCATGTGTGTGAAAAATAAAAAATAATAATGCCTCTCAAAAAAAAAAAAAAAAAAAA\r\n", "AF137051 ATCACTAAGGGCAGGAAAAGAAACTAACTAGGATTCCCCTAGTAACGGCGAGTGAAGCGGGAAGAGCCCTGCACCGAATCCCTCATCCTAGCGATGCTGGGAACTGTGGTGTTTGGGACGTCTGTTGTGGTCGTGTGCCGGAGCCCAAGTCCTCTTGATTCGGGCCATCTACCCAGTGCGGGTGTTAGGCCTTTACTGGCTTCGGCCTCGGCTGCTCTGGACTGTCCTAGGAGTCGGGTTGTTTGAGAATGCAGCCCAAAGTGGGTGGTAAACTCCATCTAAGGCTAAATACTTCCCCGAGTCCGATAGCAAACAAGTACCGTGAGGGAAAGTTGAAAAGAACTTTGAAGAGAGAGTTCAAGAGTACGTGAAACCACTTAGAGGGAAACGGGTGGACCCGCAAAGTCGGCCCGGAGAATTCAGCTCGTCGGAGGGCAGTTGCGGTGTGACTCGCAGGGGGCCGTTCGCGGTCAACGCTTGTCGCTGCTGCGATCTCGTTCGACGACGTGTGCACTTTCTCCGGGCTCGAGCGCCACGACCGGTTTCTATCGGCGGTCAGAAGATCTGGAGGCAGGTGGCCCGCCGGCGGACTCGTTTCCGCCGGTTGGGAGTTATAGCCTCCGGAACGCGGGCCGTCGCGAGACCGAGGACCGGCCGGCCGCTCTTCGCTCCTGTCCTTGCGTGCACGTTTCGACCTGCGGATACTGCCTCTCTGGGGCAGTGGCCGCTAACCGCGTCGTGCGCACCGGACCGGGATGCGTGGGCTGTGCCCGATGGTCAGTGGCGAATCGGTCGGTAGTCCACCCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGTGCGCAAGTCATTGGGTGTTACGAAACCTAAAGGCGTAATGAAAGTGAAGGCAGCCTCGGGTTCTGCCTAGGTGG\r\n", "AF204062 TGCTTGTTTCGATGTCAATCGGATGACTTTAATTTCTTGTCTGCCTCATCTTTTACTTATGGGCAATCTTCTAACCCTCCAAAATTACAAACATTTATTTTTTTTTTTACCTTAACTAGATTAAAATCCCAAAAATATCAAGTTGTTCATTTGAATTGCATATGGTAGCGATTTACTTAAAGTCGTACAAAAAATTACCGAAATGTGTATTGTCAACGTTGTGTTATCAGAGTCTGATAAATCGTCACGTAAATGCTTGTGACCTCAAAACGAGGCTTACCAAAATACTGGTATTAAATTTGATTGGTTGAAAAAATCACACGTCCAATAACATATTTGTGC" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "AAAGGTTGAGGAAATTCTATTGGAAGGTTTTTTTTAATTTACTAGAAAATTGAAATGGAGTGCACACACACACATACATGTATACATACATACATACATGTATACATACATACATTCATACATACATACATACACACATATAAACACACACATGCATGGTAGCGATGCTGTTAG\r\n", "AF204061 CTTGCCATATTGCCATGTGTGTGTGTGTGTGGGGGGGGGGGGGGGGGTCAAAGTCACCACTCGACGTAATTCGATGCCTTATGTGTTAAGTATCCTGTTAGGTAAATTTTCATTCAAGTAAGAAGTACCTGTGACAATTCCATGTAAAAGCCCTACCAATGATTGATACATGTAATTTAAAGATCCAGCATAAAATTAGGAACTTTGAATTATGTCATTAGGTACAAATAAAATGTATGCTGTTCTTTTCTTGTTATCTTTTTATATGAGTATTAGGATGAGAGGGAGATAAAAACGATCTTGGTATATCCACTGAAAACTTCTTATTTCGTACACCAATTTGCACCATCTATGCAAAGATATAGTATCAAAATCCTTNTTCTGCGTATGAGCAGAAAAAAAATAGAACTCGACGCCATAATAATTATACACACCTACA\r\n", "AF204060 CTACAATTATCATTAAGGATCCGTCGACAAATCCAAAATATCCTTTTACATTTGGTCAAAAATATATGCTTATCAATACTAAATTGGCTTCTTTATTTAATGAGACCTATACAGTGAGTGTTTGCTCATTATATTATCACAAGGTTAGCGTCCAATTACAGCAATCGGGTTTATCAATACAACATAACTTTACCATTTGCACCTTTCCAACGTATATAATGTTTGTCCCTCTCTCGCTCTCGTCCTCCTTCTCTCTCTCACATACTCTCACACACACACACACACACTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTATGTCACTTTTTCTGTTTTGTTTTCGTGCAAGGCTTCAAGTGTCATTTTATATTAACCTTTCTTTTAAACAGCGTCAAAAG\r\n", "Crassostrea AGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAACAAAACAAATCGGGGCTCGTTGGCAGAGCGACCGAGAGGCTAACGCAAAAACACAGCCGAGGGTTGTTGTTAAAGTCGGATCGACCTCGAACGCCCAGCGACCAGGTCGCTAGGCCGAGGGATCCAGGCGAACTCGCTGGAGGGTTTATCTCTCAGCGCCTTGGGCCGTCGAAGCTTTCCTGCTCCGTCGCCTTAAGTACAGACGAGCTCGACCGCGACCCCGGGCTTCCGGAACGGTGGGTCGCTAAAACAAAACAAAAAGCACTCGGCATCGTCGGGGGGAAACCTCGACGTTATAAGCACCCGAGTATGTACTTTCTCACGTATACCAACAGATTTCTTACACAAAACCCGGGAAGGCGGAGTCGGCAAGGCTCTTGCCTTTTTTCGGGGGTCGGCCGGCGTACCTCGTTGCGCGCCGCGACCGACCGAATTGGCATCATACTATTTTGACAACTCTAAGTGGTGGATCACTCGGCTCGGGGGTCGATGAAGAGCGCAGCCAGCTGCGTGAATTAATGTGAATTGCAGGACACATTGAACATCGACACCT\r\n", "AF051183 CTAGACGCCTACCGAATCCACATTCGATAACTGTAGTGGGGGGGGGGGGGNGNGTTGTTTGAAANAAAAACGTNAAAGGGGCCCTTTTCCTTATNNGNNGAATNCGCCAAANTNAAAANAAAACCGTTTNANTTTAATTTTAAAAAANGGTTAAATTGGTTTAAAACTTTTTTTTTTTTTTTTTTTTTTANCCNGAANCCTTTTTNTNTTCTTTTTTTTNTNTNTNTNTTTTTTTTTTTTTNTNTCTGGGGGGGGGGGGGGGGGGAAAGNATATTTTTTTCCAACCCTGNNAGANTGNGGGAANGTANAAAAGGGTAAANNCCCCCANNNTNNTNTTGGGGGNCCCNNCGCCCTAANGTTAAAGGGGGAANNGTTNGGGNNGNNGGGNCCCCCCCCCGGNCCAGGGGANGGGNANNAAAAA\r\n" ] } ], "prompt_number": 80 }, { "cell_type": "code", "collapsed": false, "input": [ "#uploading to SQLSHARE\n", "!python {spd}singleupload.py -d Cgigas_EST_Nuc_NCBI_040414_cl /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 151942 (2.43243002892 s elapsed)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "pushing /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing CC484ED9...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 151942 to 207445 (201.518175125 s elapsed)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "pushing /Volumes/web/cnidarian/Cgigas_EST_Nuc_NCBI_040414_clshort.tab...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "^C\r\n" ] } ], "prompt_number": 81 }, { "cell_type": "code", "collapsed": false, "input": [ "!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\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Traceback (most recent call last):\r\n", " File \"/Users/sr320/sqlshare-pythonclient/tools/fetchdata.py\", line 77, in \r\n", " main()\r\n", " File \"/Users/sr320/sqlshare-pythonclient/tools/fetchdata.py\", line 71, in main\r\n", " data = fetchdata(args.sql, args.format)\r\n", " File \"/Users/sr320/sqlshare-pythonclient/tools/fetchdata.py\", line 30, in fetchdata\r\n", " return conn.download_sql_result(sql, format)\r\n", " File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 328, in download_sql_result\r\n", " \r\n", " File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 252, in poll_selector\r\n", " \r\n", "sqlshare.SQLShareError: code: 400 : {\"Detail\":\"Invalid object name 'sr320@washington.edu.Cgigas_EST__Nuc_NCBI_040414_cl'.\"}\r\n" ] } ], "prompt_number": 63 }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "REFRESH" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!fasta_formatter -h" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/bin/sh: fasta_formatter: command not found\r\n" ] } ], "prompt_number": 85 }, { "cell_type": "code", "collapsed": false, "input": [ "cd /Volumes/Bay3/Software/" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/Volumes/Bay3/Software\n" ] } ], "prompt_number": 87 }, { "cell_type": "code", "collapsed": false, "input": [ "ls" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ".DS_Store\r\n", "._.DS_Store\r\n", "\u001b[31m._novocraft\u001b[m\u001b[m*\r\n", "._novocraftV2.07.10.MacOSX.tar.tar.gz\r\n", "\u001b[31m._samtools\u001b[m\u001b[m*\r\n", "\u001b[31m._sratoolkit.2.1.0-mac64\u001b[m\u001b[m*\r\n", "._sratoolkit.2.1.0-mac64.tar.tar.gz\r\n", "Anaconda-1.4.0-MacOSX-x86_64.sh\r\n", "Anaconda-1.9.1-MacOSX-x86_64.pkg\r\n", "BEDTools.v2.17.0.tar.gz\r\n", "\u001b[34mBSMAP\u001b[m\u001b[m/\r\n", 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warn \"\\nConverted $count FASTA records in $. lines to tabular format\\nTotal sequence length: $len\\n\\n\";' Roberts_Sigenae6_transcriptome.fa > Roberts_Sigenae6_transcriptome.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "Converted 31952 FASTA records in 451733 lines to tabular format\r\n", "Total sequence length: 24247683\r\n", "\r\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "!head Roberts_Sigenae6_transcriptome.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "AJ565441.p.cg.6\t\tGCTGTCGCTCTAGATAACATTTCCAAGTACATGTACATATCTAGCTGACCTGACTTATTTTGCAAGAAAGGAGAACAGAGTTCGAATTACAGATTTTGGATATGACCTGCAGGGATGGAAAAGCATTCTTCATATTTCTTGCCGTGGTGACAGTAATACCCCAGAAGTCGGTTCAATGGGACCCGGATGCTGGTATAGTGACGTCATGGACAAAGTATCCGAATGTTACAGTAAACGTATCGTCCTCTTCCGGCACATCTGATCCAAGATCAGTAGTGGATGACAACGACAACACAATGTGGGTTTCCGGAAGCTGCCTGCCGAGTGGCTTTGTGGGTGACCCAGAACTGAACCTGTTCCATGGTCTTTGTGACAATAACAATTTATGCTCGGTGTCAAATAGTCCCGATATTTACAAAGCGACTGATGGCAACCCATCTTACACTGTAGCTACAATTAACCCCGGACAAGATTCCTCCGAGGCCAAGTTAGTGATTAGTCTACCTCAACCCGAGGTGTTGATGTTTCTCACTGTCTGGGGTATATACAACCACGGTACTACCAAGATGTCTTTGTTTGACAGTAACAACATTCGACGGGATACAAGGTTGCTTGTATCCGCTGATAGCTACAAACAAATTTCGCTTACCAACATTTCTTACGCTGTCGCTAAGATAGAGTTTAATTCTAGTCAACAATTTCAAATCAAGGAAGTTGCTGCTCTTGGGAGCAAGGGATGCATCGCCAAACTGACACTGGATCTCGGGGACACACGTATGATTCAAACAATTCGATCACGACATTGGGCTGGACATAACACAGCCTCTGCCTTAAAATTAAAGATTTCTGAATTCGGAAA\r\n", "AJ565444.p.cg.6\t\tGTACGTAATTGCTGTTTTGTTTTAAAACAAATATTTGTTTAAATTATCAAAATAGGAGAATCGATTAAACCCAGATGCTTTCCGTCGGAGACAGAATCAAAAACTGTGAATGTAACAGAAGACAAACCAGTTGGGTTCACCGTGTTCACTTATTCGGGTTTTGATGCTGATGGAGATCGCATTAGATTTGTGTTACTTGATAACACGGTGCCGTTCTCGATTCCAACAGCAGGATCCGGGGATGTTGATGTGGCTTTACCTGCCTTAGACTTTGAGAGGAAAACTCAATATATTTTGGACAAAATATACGTCACTAAATTTGGATTGAGTGCACTCCTGTTTGGTAATAAATGTGGAACCCTAACCGTCAATGTCCTCCCTGTCAACGAATTTACGCCAGTTTTTGATCCCTCATATCAAAATTCCTCACTTCCAGAAGGTCTACTACAAAATTCATTGCTTGCTAAACTGAATTGTTCTGATGAGGACAAAGAACCCAACGAATCCCCTTTTGGATGTTCATCAATAACTATTCAGACTGGAGATGACATTAAACCGAAATTTACGATAGTCAACAACGCTGTCGTCACAACAAACAACGTCATTGATTTCGACACTGGTGACGTCATTTACACACTTGTCATAGTTGGTGGTTGATAGTTCAACACGTGATCCACGTAAAACAGGAACGATGACGATAAAGGTCATCATTGAACCTGTG\r\n", "AJ565448.p.cg.6\t\tGGTTATTTGCTACTCTTGACAGCCCGGTTGACGAAAATCAAACACCAAGTGTACTGAGACTCTTGTCTAGACCGATTTGTGGGGTCAAGGTAAATTAGATGATCCTCTATACAATGGATTCATCATTGTCATTTAAGCACCAAATTTTTATTGGAATAAAGATTGTACATCATTTTACTAAAATGGTTCACAAAATAACCTATTTATCAAGAATTTATTGCATATTTATACTAATTAATATTTGGATAACCACATGAACAAAATGAATCAGATTTAAAATTGTTCTAAAAGTATTCAACTTTCAGTTAAAATATTTATTTATATTATATTTAAACATTGATTTTTAAGCAAAAAAACTCAATAAAAGAACTGTTGAATACAACATGAGAGTAACTGAAAATTATTGATGTTAAGGATGTCTGGGATAAACAAGAGGTCATTAAACATTATTCGGACACTAAATTTCACAAAAGATTATTATTTGGTATTTATTACAGACAATTTGACTTGAAAATTTATTTTGAATGCTAATTCAGACCAGAGTATAAATTGCACATCATTTTGATTTTAAATTTAAATGCTGAACTGCAGGATGAGGTTAATGATGACTATTTGCTACTCTTGATGTCACACTGATGTCAACTATCACCATTTTCTGAGATCTCATCTGTAGTGTATG\r\n", "AJ565449.p.cg.6\t\tACCCAAACACACAGCCCATCTTCTTCTCAGAAGGTTTCCAGATGAATTCAATTTCACTCACAGTTCTGCTGCTCTGCCTGTTTGCAATCAGCATAGCGGCCGGATGGTGGGTTGAAGGAGAATTGGACCTGTTCATAGCGAAAGCAAAAGTTGGTTTTCTTTTTAAAGGCAGGAGAAAGAGGCATATTGCAGAGGAACAAGTCTTTAACGTAGTGATGTTCATGGTAAACGAAAAAACCGGAAGTAGATTTAGACTCAACCCATGTGACTATGCGCTATATGACCAAGACGACGACTTCACGGTCACGCCGAAAGATTTTGATATAATATTCTCTAAAATGGATAAATCAAAACATATTTTGGTGGAACAGCTTTTCCGTGAATTGGATATGGATAATGATCAGAAAATTTCCCTAACGGAATTTGAGGAAAAAGAAGGTCTTGTTTTCTCCAAAAAGACGTGCCTTATTGACGTGTTATATTCATGACTTTTTTCTGTGTTTTCTTTTTTTTTTTTTTTTTTTTTAAAGTAAAATTGATTATTATTTGTTCTAAAACGAATTATCGTATTCTAAAAAACCTGTGTATCTTATTATCAATTATTATCATTCATATATTTGTTTCATCTGGAATATCGATATATGTCCGTGAAATACATGCCTTTTTGTCATTTTTGTACTC\r\n", "AJ565453.p.cg.6\t\tGGACTCCCTCTAGATCTTAGCATGAAATAAGCTTAGCTAATGCATGATCTTGTTTTTGTATATGCCTTGCAATATTATGTAGAAATAATCAATGTGATTGAGCATTTTGGTGTGAATAATTGCATGAATTGTTATATCATAATCTGTAATTTCACCATTAAAACTAGTGCTCTACTC\r\n", "AJ565458.p.cg.6\t\tGGGTGGAATATTTGTTGGAGCATTTCTTCTTCTTTCCTTTATCTCGTTGGTGAAAGGAAACTGTTCTTTTTCCCGCAACTTGGCTGGAAACTGGGTAATAGATAAAGATGGAAAGGAACTTGGGCGCATGTCGATTGGCTACACAAGAATGGACGTGAATTTTATGGGCCAACGATACAACTACACCTGTAATCAATTTGACTACAGTGAAGAAAAGTATCTACTGAGGGCTACAAATGGGAATGGGATGGCATGCCTGTTATTCACACAGTTCAGTGATGGGGGCTCCACTCTTATGATGATCCGTCTGCACATGACCCACCACTATGAAGATAAGAATTTCTTCAAGCCCCAACAAGTAGCGGGATCTCCAACCATGAACTCAGTGTGTAACAATTATGACGATGGACAAATGCTGTTTATTCACTCTGTGCCCTGAATTGTCTTACATTATTCTTACATTATTCTTGATTGTGTTTGATATATTTTTAGAATTATCTGTTGCACATAGACTATAGAAAACACCTGTTTATATTTTGAAATTTAGCCGACAATAAAGTATGGTTAAATATGTTTTAAAGACAATAAAGAAAATGATTTT\r\n", "AJ565465.p.cg.6\t\tGCACAGACCAAGGATCAGCACACTGGAATCAGCTGTTAGTGGAGATGGACGGCATTAATACGACAGAAGGAGTGATTGTGCTGGGGGCCACAAACAGGGTGGATATATTGGACAAGGCCTTGCTACGTCCAGGAAGACTTGATAGACATATCCTTATTGACCTCCCCACATCTGAGGAGAGAGTGGAACTCTTTGAAATGTATTTGTCAAAGATTAAAATAGACTTCTCCATTTCTGTATTTGCACCACGACTAGCACAGCTTACACCCGGAATGTCAGGTGCTGACATTGCAAATGTGTGTAATGAAGCAGCCATTTATGCTGCGACCAACAACAAGGATCAAGTAACAATGGCAGATATGGACTACGCTCTACAGAGGATCATCGGCGGTCCAGAGAAGCGATCTTTTGTGAGAGACGCCCGCGAGAAAAAGATCAATGCGTACTACGAGGCAGGAAGAGCTGTGGTTTCGTGGTTGACCAGAACTTCTGATGCCATTTTAAAGATTTCAATTGTACCTAGAAGTAAATACAGATTAGGCCATTATCAGTATTATAAGCCGGAGAGGGATCTCCAGACTAATGTGCAGTTATTTGAGAAGATGCTTGTCCACTTAGCAGGCAGTGCTACAGAGGCTCTGGTTTTCAAGCACCATTCCACAGCTGCTGAAAAAGATCTGGATATTGTCAAAAAACTTGCTTACCTACAAGTTAGAGGAATTTGGAATGAATGAAAATGTTGGCCAAATCTCATTTCATTTCGAGGGAGGGGGATGAAACCCTCCCTAAACCCTACAGTAAATACATGGGAGAATATGATTGACACGGAGGCAAGAAATTTGGTTACAAAAGCTAGTGTGCAG\r\n", "AJ565467.p.cg.6\t\tGGTTGGTGATATTTAGGAAAAGAGTGAAACAATTGTGGTGCTTAAAATGCATTCTCCTACATAACAAGAAAATGTCTTTCATCTGTATTAGCGCAAGATCAACGTTCAAGATATCCGCTTCAAAGCAAAACCATCGAAGAAACCACGCAGAGGTAGATGAATTACGAGGGCGAGAAAGAAAAAGCATCAAGAAAAAACTCGACAAGGGGCATTACTCTCCTATTAAATGAGGAGAAGAATCGAATCAAAGAACGTCATCGGAACCCCAGCAGTGACACCAACTTTTCGAACTCAGATGCGGGAAAAGTAAGGTTGGAGACAGAATGTCTACAAAGCAAACAAAATGGCGTCCGTGGAAACTCGTTAAAGGAATCACTAGATACCATATCAAGATATACCGGAAGCTTTGAAGAATTTGTACAGAAAGAAATATCATCAAATAGAGATCTAGAGAACCAAGCACATTCATTAGCATCACCATTGTGTCATTCCATGAACATGGAGTTAATCCGACTCAGGTCTTTCCATAATTTCCCGTCCTCAAAAACTATTTCTACACTGCGACTGGCTCGCAAGGGATTTTATTATTCTATGGAGTATGACGTCACAATATGTTTTGCTTGTGGTTTTCGAAAACGAGACTGGAGGTCTGACGATGTCATTGAGGTTATTCATCGTAACATGTCTCCTGACTGTCCCCTTCTGTCAGCACAGCCGACCAGTAACATCCAAATTGGAAATGACCAAAGGGATGGGCATTGTATAAACGAACTCGAGCAGCAATTTAACGCTAGTGGTAACGAATTTCCTAGGAGAAGCAATAGACAGCCATCCCTCTTCAACCTCAGAAATGCTTCGTCTGGACATG\r\n", "AJ565474.p.cg.6\t\tATATAAAGCAGGGATCTGCTCAGGAAATTGCAGCCTGTAGAGAGATCCTCATCTCTTCGCATTGAAAGGCCAACTTCACTTGTTATTCGACAACACAGAAGAAATAGCCTGCCTAGTCCTTCTGTTATCAAGGCAATCGTCCATATACCGGACTTGGAAAGAGTCCGGTCTTTTAGTCTTACTCGAGACGGACTCAAAAACTGCGGGGACAAAATCAGGCGACGCAGTACATATAGTATTGCAACAAGTGAGGGGCCTGATTCACTTTCCACCGGAGCAACATCTTCTTTGGAAAGCATCTGTCAGAGGCAACAATTTAAGGTTGCTATCATAGGATCTGCAGGAGTTGGAAAAAAATCGTTGAAAAATCAATTTGCAACTTCAGAAGAACTTTACATAAACAATAAAAGTAAGTAAAAAAAAAGATTGGTAAATATTTCCGTTTATCATTTATCATTTAAAGCTATATGCGGCATATTTTTTCATGCTAAGAAATATTTGATTGATTTATTTATTTAAATATGTTATATAAGATATATCTTCACAATAAATTACGCAGTTTATATCAATCGGGATAAAAAGATATAGAAATTAATAAATAATTTTTAAAATTATTTTCGATTCCACGATAAATAGAGCATTTGAATAAACCCCGCCTTAAATCGGCCACGTGATACCACGAAATTTTTGAATAAAGAATAAATAAAAACTCTCAGTACATGCATCCCTCAGGAAGAGGGTGTATTCATAAATTTTATCGTGTCGTTGATGC\r\n", "AJ565485.p.cg.6\t\tGCTTCAATCAGAACAAAGTATTATATTTAGATATATGTTGAAATGTTTAGGAATTAGTATTAATTTAAATTATAAATTATAAAAATAAAGAAGTAATACAATG\r\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {spd}singleupload.py -d Cgigas_Sigenae_v6 Roberts_Sigenae6_transcriptome.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 31952 (0.137900114059 s elapsed)\r\n", "pushing Roberts_Sigenae6_transcriptome.tab...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing C6E51C88...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Traceback (most recent call last):\r\n", " File \"/Users/sr320/sqlshare-pythonclient/tools/singleupload.py\", line 42, in \r\n", " main()\r\n", " File \"/Users/sr320/sqlshare-pythonclient/tools/singleupload.py\", line 39, in main\r\n", " conn.uploadone(args[0], datasetname)\r\n", " File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 181, in uploadone\r\n", " \r\n", " File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 202, in upload_chunk\r\n", " \r\n", " File \"build/bdist.macosx-10.5-x86_64/egg/sqlshare/__init__.py\", line 244, in poll_selector\r\n", " \r\n", " File \"/Users/sr320/anaconda/lib/python2.7/httplib.py\", line 1045, in getresponse\r\n", " response.begin()\r\n", " File \"/Users/sr320/anaconda/lib/python2.7/httplib.py\", line 409, in begin\r\n", " version, status, reason = self._read_status()\r\n", " File \"/Users/sr320/anaconda/lib/python2.7/httplib.py\", line 365, in _read_status\r\n", " line = self.fp.readline(_MAXLINE + 1)\r\n", " File \"/Users/sr320/anaconda/lib/python2.7/socket.py\", line 476, in readline\r\n", " data = self._sock.recv(self._rbufsize)\r\n", " File \"/Users/sr320/anaconda/lib/python2.7/ssl.py\", line 241, in recv\r\n", " return self.read(buflen)\r\n", " File \"/Users/sr320/anaconda/lib/python2.7/ssl.py\", line 160, in read\r\n", " return self._sslobj.read(len)\r\n", "socket.error: [Errno 54] Connection reset by peer\r\n" ] } ], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/GPL11353_v6fasta.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Column1,Column3\r", "\r\n", "CU995582.p.cg.6,GAAGAGCTCAGTGTTCAGATGACAGAGTTTGGATTCCGACGGGTAAAAAAGACGGACGATGGTTCCTATGGCAGAGTTTCCAAAGACCCGTCACAGTGTAGTGTCAGATCGCTGTTATTTCACAAATCTGGCTCACTGTCAGCCAATTGGACTCCCAAGTTTGACGGTGACGTAAGACCACGAGCAGGCCTCGTTTTCGTGGAGCCCAAACTTTACAACGAGTATCTAAAAGAAGAGGCCCAAGTACGTCATCAGACCGCCATGATGGCGCGTAGTCGTTCCACTAACATCAACACATTAGAGGACGATGCCACGGTTCTAGAAACCGTAGAAACGTGACAAATGGAAACAGTGTAGTTGTTTAGTTTTCATGTTCAAGTTTGCAATTGTTTAAATGTACCAATTGCGTGTAAATCACTATATGACGTCATTTCTAAGTAATACTCAAACTCTGACAATTATCAAATTGAGGATGGGTCAATGTTTGTAACTTGAATGACAAAATCAAACCTTGAAAATAATACTAGGAAATTAATTTATTCATTTTGTTTGTCAGTCTTGATTGGGAAAATTCAAGATTGCCCTGTTCTTAGTTTATCACATTGACATTATACATGAATGGTTTCTACTTATTTAAATTCTCATGCTGGTTGTTTTTTATAATTATTTATCTATGCTGTAACATTCCAATGTTAGGAAATCTCCACGAATCTAGACTTTGATAAGCCCCCTTCTTTCCACTACATCCTCTAGAACCTTACAAGAGGTTATCTATCCCTTCCCTTTAACTAGGAGGAAATGTGTGTAAATAAACTGGTGCCCCAACCTGTAGTTGTGCCTGTTCTACCAAAGTTAAATAGCACCTCCTAAATTTTCCAATGGTATAATTTAATAAATTTCCTTTAAACCCCCGGTTTCCAAATGGCCTTGGGCCCTCCATTTTTCCCTATAATAAGGACCCGGGTTGGCCTTTGGTCCTTCCCCCCCCAAAAATTGGTAACTTTTTCCCCTCCTAAAAAACAAAGTTCACCTCCTGGAATTTAACAATCCACTCCCCCGGGTTTTTCCCTTTTTAAAAATATAAAAAACAAG\r", "\r\n", "AM862909.p.cg.6,GGTAGGAAAATGTTGAATATTGTTTATATTAACTATTGAACAATACCAGTTAAGAAAGAGACCATTGCATGTAACAATTTCATTATTTGGAAAACAACGGACTAATTATTTTTCTTTTAACTTTCTCGTACAAATTGCATACAGGAAGTTAATACCGCCACAGTAACACGGGAGGTAACTCGTGATACACGTTCAATCTCAAAAAGTTATCTGAAGTAAACGCACATACATATTATAGCACTGAAGTATTTCAATCATTTTTGTTTGATATAACTAGTAAAGTTAACATAATTAGATGGTTGATTATACGCAAAGTGATGTTATATATATTTAACGACTGAAGAATTGCAACAACATTAAAACTTAACTAATCTTTAAATTTATTATCAACCATGGTAGGGAAAACCAACCTTCTACGCTCTACTAATGTCATTTTCAGACATTATCATGACATGTACCAGATGAAATACTACATACAAAAAAATAGAAAACCAACAATTTTTTGGTTTACATTCAGAAAATAATATCTGTAAATTGTTAAAATAAAGTAACATGTTAGTTTCTTATGTAGAATAATAATTTTCCACATTTCTTT\r", "\r\n", "CU991229.p.cg.6,GGATTGTAAGACAGAATATGAATGCCAGATCTCGACTGGAATCTCAAAGAGAAGAGATATTTCGATACATAAAGAAGTCGTCAGAGAGTCATCACATGGAGGCCCGACTACTGAAAGAGGACCTTCATGGATTTGTGAACAAAGAAGTGGACAAGTTCGCCTCTCTAGACCTCCCTCAGCTCCTGTTCTGTGATTCCTCTGACAGGGCTCTTAAAGTAGCTGTCACAGACATGTCCATACACCAGACTGGTGCCCTGACTGCACGGGAGGCCATGAACCAAGTTCTTCATCGTCTCGACTTCAGAGCTTTTCAGGCCCCAGAGCTGCTAGTGTGGAGCTGTATAGAATTAAAAAGAAAAATCCAAAAACTGCAGAAATTGTCTGCCCCACTGAAAATACATGACCAGGATGGAGAGAGCATAAAACAGATTGCAGGACTGTGTGAGAGAGTTAAGGATCAAGACAAGGCTCTGTTGGAGAGGACTCTACCAGTGTTACAGCAGAGGCTACACAAAACAGGGGCCGCCCTAACGGACTGTAGTATGGTGTCAGAGAGGATTCAGGAATGGTGGGAACAACCAGCCCAGCATACCGCGCCCTGGGTCAAAGTGGACCAGAACACCCTCCAACAGTGGCACACCAGGTGGACCGTCCTGTCTACTAAATACAGGCAGCTCCTGCTGCAGAAATCTTAAACAATTGTTGCAGCATACATGTACTCCCTAAAGATTAGAACAGCAGACATAGGCATACCCATCTGTATCATGTCTAGTAGCTATTGCCCTTGAATTATTAGGAATTAAAAAGATACAGGTGATAAATAAATGTATCAGTGTATGTATGGTTGTAGTTATATATTAAAATATTTGTACAAAAGTATTTAAGACCCCTAAGAAATTTGAAGTTTAGGTTAACTTTTTAAAATGGAAACGAATCATTATAATAAGAATGGCTCCTGCTTTGAAACAGCAAACTTTCTTATTTATTCAAAAAAAGTTTTTGACCGAATTGGGTATTTTTCCATTTGGGCTTTTTAAAAAACATAATTCTTTTTATTTTAAAATACAAAAGGTTGCCTTTTTTGGAAGGGGGGGACATTGATTAAATTTAAAAATTTTTCCAAAAACCTTTTAAAAAAACCAAAAAATTTTCCCTTGTGTTTTTTTATAAAAATGTGTTGAAAAACCCCCCTTTTTTTCCCTGCCTCTTTTGGTGGGGGGGAAAAAAAAA\r", "\r\n", "AM863560.p.cg.6,TTCGCACCAGAAGCAGTTTGATTTTATATATCTCAAATATACAGGCACCATGTCTTACAGAGACTTGAGAAATTTCACGGAGATGATGAGGGCCTTGGGATATCCAAGACTAATCTCCATGGAAAATTTTAGAAACCCCAACTTTCCTTTAGTTGCAGAAGTAATGCGATGGCTTGTCAAAAGATATGACCCGAATGCTGACATTCATTGTGACATCGACACAGACCAAGACAGAGTCATTTTTATAAAAACTGTGGCAGAATTCATGCACACAAAAGCCCATATCAAGATGAACACAAAGAAGTTATACCAGTCTGATGGGTATGCTGTTAAGGAGATGCTGAAGGTTACCTCCATGTTGTACAATGCCATGAAGACCAACTCATCCAGCCAGTCAGAGACTGACAATGAAGACGACTCATCACATCTTTCATTTGATATCTCATCAAAGATTAATGATTTAAAAGAAGCAAGAAGACTGGCATCAGAAATAACCACCAAAGGAGCAACTTTATATGATCTTTTNAGGCAAGAAGTGGACCTAAGGGAGCAAAGATCCATT\r", "\r\n", "AM868645.p.cg.6,GGTCGTCAAAGAGGTCAGCTGTGGAAAATACCGAGCTGTTGTCACTGAAGTCAAAGGTCATGGTTACTTTTGTGGAAATTCGACTTTCACCTTGGAAGAAAACGATGTCACCGGAAGAGGGTTTCTTTTACAGAAGCATCCTTGCAGTTAGACTTACCTATTAAACACATGGGTATTTAGAATAAAGTAGCTGCCTTACTTATTGTTCCTTGAAGGAAAAAAATCAAATCTTATATTTGATGATGCTGTTTTATACAAATCATACGTTTTGGAATCTTTATAGTCGTTGCATTCACACTTCTAATAATAGATGTATAAAGTGAAGTTGCTTTACGTTTAATTAACATAGTTATATTAATGTTGTGTTGTTTGAATACCAAATTGTTGCAATAAAAAATCTGCTACAGAAGAACAACAAGGGTTCTTGTGGTCAGAAGGGTTGGCCAAACACTGGCGCAGGCT\r", "\r\n", "AM856822.p.cg.6,AGCCCACTTAATGAGTGTGGACGGGAAAAAACTGTTGATTTTCAGTCTGATTAATTTATCCAGAATGTGTACACATTTTCTTAATAGTGTAGTGTTATCCTTATTGCACGTAACGTTATTACGTCTTGTGGATTCTAAAAGGGGACCATGCATTCAGTATCCGAATGGATGTTGTCCATCGACAATGTGGGATACAGCAAAGAAACAATGTGTCGGTAGGCTTAATACCTGCATTGCTTATAAAAAGAACACGTGTGATGATTTTGAAACAACGTTTGGGTGCTGATAAATTGAAGATCATCATTTGACCTGGTTTTTAAAACGCTAAGCATTATAGCTCGGTACTTATTTGTCGTTAGACGTCTACGTCCGGTGCACTGCATAACCGCTCACATAGAACAGAAGTATACATCATTTAAACTGGTTCGGGGTTAATGCACATAACTGAACAGGCTATTAATGTCCATTAGGTTTCTACTGGCTTAACTGCAGTAGAAGGTGTGTTTATCCTTACTTTGGATATAAATGTCAAGACTATTGTTTCTGTGAAAAGGACCTGTGTGACTTTGTGAGAGGATGCCTTGGGTATATCGAAAATTCGACAAAGCAATTGTTGTCCAGTTGTAAAAACGAAATTGCAAAACCAGATGCAGATAAGAATTCGTTCGTAACAGTTTTAACGGTCATAGCAGTAGTCTGTATCGCGTGTGTAATGGTTTTTCTCTTCAAGGAACCTCGTCAAGACCACAGTGATAAACACAACCACAAATAATGTAGGTTATTAAGATTAGAATGACTTATCAGGGAAACTTTAATTTATTGATTGTTTCTCTCAAGCACTTATTT\r", "\r\n", "FP006184.p.cg.6,GGGGACTCTAAGTGGTGGATCACTCGGCTCGGGGGTCGATGAGGAGCGCAGCCAGCTGCGTGAATTAATGTGAATGCTACCAGGACTTTCGATTGGCTCACTATCGGACATACAGACGGAATTCTTGGCCGATCATTGGCTATTCTCCAGGGAGACCACACCTCTCACACCGCTGTCATCGCTTGCTGCGTCATTGGTCGCTCTCATGCTCACTAGTTGACCTAACGGACCATTCTGAATAAAAGATTATCATTTATATTGGACTTCAATAGAAATAAAAACTTACC\r", "\r\n", "AM862004.p.cg.6,ATCACATTCTCTGACTTTGACAAGCTCTATAAGCATGTATCAGCGAAAAGATCCATGGAGAGTGAAAAAGATGGGAAGGTTAACAACCAGGAGAAAGCAGTGGAGGTCAAAACTAAAGAGAAAGTAGGCAACAGTGAAAAGGCAAGTCAAGAGGATTTAGACTTCAAAACTCCGAGCGTGCCCAGCAGGAAGAGTACGAAGTCAGCGGCCAAGTCCAGGTCCAAGAAAAGCAGTAAAAAGAAATCGAAAGATGAAGAACAGAAATCGGGAGAAGTGCAGGGCTCAGAGAAGGAGAATTCTGTAGAGCAGAATGTAAGTCAAAGCAAGAAGAAGTTGGAGCTGCTGAAGAAGAGGCTTACAGAGTTTGATGCCAGGAAGCCCTCCCTAGACCCCCTGTCTGACGTCACAGTGACCAAGTCCCTCCCCTCATCCCCCAACCACTCAGAGGAGCCAGACAAGAAGAGGCCACGAAGAGGGGGCCCTATATCATACAAAGAACGGCCCCTCAACAGTAAAATCAGGAGAGGAGATGTGTTCTTTGAGTGAGCTGATAAAATTTACATCAATCCTACAGAAATCTGGCAGATAATAGAGAAATGCAGCAGCTTGGAGCAGAACCCACAGCTACGAGTGCTGAATGATGCGAGATTACACAATACATGTGTGTGTCATGGCCGAGTTTNCAGTGTTTTTGATTACTTAGTGGAGATTTTATTTTTATAAAAAAATTTTTCTTTTTTTCCATAATGCAAATAAACATTTTCCTCTCTTTTATAGCCATAAGTACAATGTAATGAATAAATGCATG\r", "\r\n", "CU998134.p.cg.6,GATATGTCCGGATATGTGTAGCCGCGGTTAATCTTACGTTACAAGATTCTCTATATTGCTGTTTACCAGAATGGGTGCACAATGAGAAATTGCAAACATATCTGAACAAAATGATTTGTTTTCCCACTTGTTTTGTTCAATTTTTGATTCCTTTAAGCTGGAATCACCTTCTTTCAGAACAGGGTAGAAGATTTTCAAAGGAAGATTTACTTCAAAAATTATTTTTTTTTTTTCAAATGTTAAAGGCTTTATGTCATGAAATTTGCTTTTGGGCCTTTGGTGAAGACAACATGTAAACTGTCTGGGTTTTTGTTTGCCTGTTATACCGGTACCATGCTATTATGGCAGATTGTTTCTCTTCAGTATATTTCAATGTTTAGCTGTTTGTTGTGCCATATATGGGAAAAAATATCAAAATCTGTATGTATTTTTAATTTAATATGCTTAAAATTTATTGCATAATTGAAAAACATGAATACCATTGTTCTATGCCGTTTTCTTTTTCTCAGCAGGATCTCATGTTATTGTTTAAAACAATGGCACTTTTGACTTTTGAAATTGATACCGAAAGAACATAGTTGTTTCTGTTAAATCATTATGTTCTGAATATTTTGTAAAGCTTCAATTATTTATATGCGATAGAACTTTTTTCCACAGCAGAGGATAAAAATTCTGATATATGTATAAGTGTCTCAACACATGATAAACTCTTTATATTACATTGTTGTTTCTGCGACTCTTTAATAATCCGAAAGTTGAGACCTTACTCTACCACCTTGAAATGGAAGACTCCCCCACCTTGAAAGTGAAACTCCCCAACCTTGGAAGTGAAATTCTACACCTCCGGAGTGGAAATCCACAACCTTGGAATTGGATCCCCCCAACCTTAAAATTGGAAATGCTAAATTGGCATTTATAATTAAATTGTTTTTCTTTATTTAACCCGAAGTCACTCATTTCCAAATTCAAGGGTTTGGAAAAGTTTCAAATGGGTTTTAAAA\r", "\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk -F \",\" '{print \">\"$1\"\\n\"$2}' /Volumes/web/cnidarian/GPL11353_v6fasta.csv > /Volumes/web/cnidarian/GPL11353_v6fasta.fa" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail /Volumes/web/cnidarian/GPL11353_v6fasta.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">AM860865.p.cg.6\r\n", "CACAGTGTGAAGCTGTTACATGGTTGCAGCTCAGGTGATGGGAAACCATGTTGCAGTGACGGTAGGTGGAAGTGACGGCCATTTTCAGTTGAATGTATTCAAACCAGTGATCGTCACAAATGTACTACAGTCTGTTAGACTGATCGGAGACTCTTGTGTGTCATTCTCCAAAAACTGTGTGGATGGAATAATACCGAATACAGAGAAGATTAATCGTTTTGTAAATGAATCTCTGATGCTGGTCACAGCACTGAATCCACACATAGGGTACGACCGCGCGGCAAAGATAGCTAAGCATGCTCATACAGGGTCCGCGTTAAAAATGGCCGCCGTGTCACTGCAGATGCTGACTGAGGAGGAGTTTGACATCAAAGTTCAACCAAAAGACATGTTAGGACCAAAGTAATGCCACTGCAGCAGAACAAATTCCTAGACCCAATGAGAGTCATTCGAACATGTATTGGTGGTACACATGTAATAAAATTCAAATCTTGCAAAGAACATACATTAATGTTTTATTTCATCTGTTGGTCTGTGACAATATTTGTCATTCCCAATATTGTCCCCATAATTTTTTCTGTCTTC\r", "\r\n", ">AM869341.p.cg.6\r\n", "ATTTTGCAAGATTTTTGTTGGCTTATAAAGTCAAATTTTGTCGGCTAGATGGCTACCCCAGTATCCAGGAGCGCCAGGAGCAGATGGCTGATTTTAACAGGAATCCATAGGTATTCATTTTCCTGTGAAGCACTACAGCTGGAGGGTTGGGGATCAATCTGGTTGGGGCAGACACTGTGATCATATACGACAGTGACTGGAATCCCCAGTGTGATCTCCAGGCCCAAGACAGGTGTCACAGAATAGGACAGAGTATGCCTGTGGTCATCTACCGCTTAGTGACCACCAACACCATTGACCAGCGCATTGT\r", "\r\n", ">EE677551.p.cg.6\r\n", "ACCTTTGAACATTAACACTCTTTCACATTACAAAATGCTCATATTACAACACCTAGTATTGACACAATTGCTCTCATGATTACAACTCTGTATCAAACTAAAAATGCCAAGTACCAATTATTAATAAGTTTATATGGATTAGTCCTTTGGTCAGTATTTACATGTCCTCTTCCTCGGCTCTGGTCGGCGCCACGAAGGACAATCTGCCCTCGGGGTCACGACTCACCTTGACCTGCCTGCACTCCATGCCCTCGGGT\r", "\r\n", ">AM860135.p.cg.6\r\n", "CGGCAGAACCAGTGGCTGGCCAAAAGGAACAAATCCAGTGTCTTATGCAGCTAAATATGGCATAACGAACCCTTCACCTACGTTAGATCGCCCGATCAATCTGTACCCATTAACAAATTACACATTTGGAACCAAAGAGCCATTGTATGAGAAGGATAGCTCAGTCCCAGCACGGTTTCAGCGTATGCGAGATGAGTTTGAGAAGATTGGAATGAGGCGATCTGTTGAGGGAGTGTTAATTGTACACGAGCACGGACTTCCCCACGTTCTCCTTCTACAACTAGGGACCACATTTTTCAAATTACCTGGGGGAGAGTTGAATTCAGGCGAGGATCAAGTAGAAGGCTTGAAAAGATTATTAACAGAGACCCTGGGAAGACAAGATGGTGGGACTATGGAGTGGGTAGTGGAGGATACTATAGGGAACTGGTGGAGACCAAACTTTGAACCCCCACAGTACCCTTACATCCCAGCACACATCACAAAACCCAAGGAACACAAAAGACTTTTCCTTGTACAGCTACCAGAAAAGGCATTGTTTGCTGTTCCTAGAAATTATAAACTTGTGGCCGCCCCCTTGTTTGAACTATATGACAACAGTGCAGGATATGGGCCAATCATCTCAAGTTTACCTCAAGCTCTAAGTCGGTTCAACTTCATATACAATTGAGTGGGAAGATGCGAAGAACTGTACAACAATATTATTGTGACTTTTTTTATTACTCTGTCTGTAATACTGTCAGCTGTGGCTTGTCAACTTTGTATCACGATCATATCATCATATAATTATATGATTCATCATGGTCGAAAATGTCATTGAGGAATAAAAAAAAATTCAAACAG\r", "\r\n", ">BQ426856.p.cg.6\r\n", "CCTGAAACAACCAAGCAATTTTAGAGATCTGTCAAAACATATAGGTGCTCTGAACCCCACAAGAAGAGAATTTTTTCAGGAGCGTTATAACTCATGGGAGCATGATCAAATCCCACCATTCCATTATGGCACTCATTATTCAACGGCAGCTTTTACTCTGAACTGGCTCATAAGAGTGGAGCCATTTTCTACAATGTTTTTGAACCTTCAAGGTGGCAAATTTGACCACGCCAACAGAACCTTCAGCTCTATAGCTCAGTCTTGGAAGAATTGTCAGAGAGACACTTCTGATGTGAAGGAGTTGATCCCTGAGTTCTACTTTCTCCCAGAAATGTTCATCAATCAAAATAGGTACAAGTTTGGAAAGCAAGAAGATGGCGGAGAAGTTGCTGATGTGGAGATGCCACCATGGGCCAAGAACCCTGATGATTTTGTCCGAATAAACAGAATGGCCTTAGAATCTGAATTTGTGTCTTGTCAACTTCATCATTGGATTGATCTGATATTTGGCTACAAACAAAGAGGTCCAGAAGCAGTGAGGTCCACCAATGTCTTCTATTACCTGACCTACGAAGGCAGTGTGAACCTGGAGAGTATGACTGACCTAGTCATGAAGGAGGCCATAGAGAACCAGATTAAGAGTTTTGGACAGACCCCCACCCAGCTCCTGGCTGAGCCCCACCCTCCCCGCAGTTCTCTGATGCACTTGACTCCGATGATGTTTTCGACAGTCCAGGATGATGTGTGTATGATCATGAAGTTCCTGTCCAACTCCCCGGTCATTCACATCGCCGCCAACACCCACCCTGCCGTTCCCAACCCCGCGGTCACAACCATCACATGTAACCACAACTTTGCTGTCAACAAATGGAACACCACATACCAACTAACCAACACTGGCCTTCAGAGACGATCCCTAGGGGACAACTTTGACGAGAGAATAAAACCTACCCACCAGAGCTTTGTCACTTCAGCAGACAACCGCTTCATCTTTGCCTGTGGATTCTGGGACAAGAGCTTCAGAATATTCAGTTCCGAGTCTGGGAAGATCCTTCAGGTGGTGAATGGCCACTTTGATGTGGTGACCTGTATCACGCGCTCTGAGTGTAACCTGAATCAGGACTGTTACATTGTGACCGGGTCCAAGGACTGTACCGCCATGGTCTGGATGTTCACCTCAAGGAACCAGGCCATCATAGGCGACAATGGAAGTC\r", "\r\n" ] } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGoRNA_array_v6_tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\"Name\"\t\"Chromosome\"\t\"Region\"\t\"Expression value\"\t\"Gene length\"\t\"RPKM\"\t\"Unique gene reads\"\t\"Total gene reads\"\r\n", "CU995582.p.cg.6\tCU995582.p.cg.6\t1..1092\t4\t1092\t0.236\t4\t4\r\n", "AM862909.p.cg.6\tAM862909.p.cg.6\t1..595\t0\t595\t0\t0\t0\r\n", "CU991229.p.cg.6\tCU991229.p.cg.6\t1..1230\t148\t1230\t7.767\t146\t148\r\n", "AM863560.p.cg.6\tAM863560.p.cg.6\t1..562\t101\t562\t11.601\t101\t101\r\n", "AM868645.p.cg.6\tAM868645.p.cg.6\t1..462\t2\t462\t0.279\t2\t2\r\n", "AM856822.p.cg.6\tAM856822.p.cg.6\t1..846\t0\t846\t0\t0\t0\r\n", "FP006184.p.cg.6\tFP006184.p.cg.6\t1..287\t16\t287\t3.599\t16\t16\r\n", "AM862004.p.cg.6\tAM862004.p.cg.6\t1..808\t132\t808\t10.545\t132\t132\r\n", "CU998134.p.cg.6\tCU998134.p.cg.6\t1..1001\t772\t1001\t49.783\t772\t772\r\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiGoRNA_array_v6_tab.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ID\tSig_No\tGene length\tRPKM\tUnique gene reads\tTotal gene reads\r\n", "CU995582\tCU995582.p.cg.6\t1092\t0.236\t4\t4\r\n", "AM862909\tAM862909.p.cg.6\t595\t0\t0\t0\r\n", "CU991229\tCU991229.p.cg.6\t1230\t7.767\t146\t148\r\n", "AM863560\tAM863560.p.cg.6\t562\t11.601\t101\t101\r\n", "AM868645\tAM868645.p.cg.6\t462\t0.279\t2\t2\r\n", "AM856822\tAM856822.p.cg.6\t846\t0\t0\t0\r\n", "FP006184\tFP006184.p.cg.6\t287\t3.599\t16\t16\r\n", "AM862004\tAM862004.p.cg.6\t808\t10.545\t132\t132\r\n", "CU998134\tCU998134.p.cg.6\t1001\t49.783\t772\t772\r\n" ] } ], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "spd=\"/Users/sr320/sqlshare-pythonclient/tools/\"\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "#uploading to SQLSHARE\n", "!python {spd}singleupload.py -d BiGoRNA_array_v6 /Volumes/web/cnidarian/BiGoRNA_array_v6_tab.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 31918 (1.10805797577 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/BiGoRNA_array_v6_tab.txt...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing F8132D65...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished BiGoRNA_array_v6\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "!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" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ID\tSig_No\tGene length\tRPKM\tUnique gene reads\tTotal gene reads\tID\tRow\tCol\tProbeName\tContigName\tGB_ACC\tDescription\tSEQUENCE\r", "\r\n", "CU995582\tCU995582.p.cg.6\t1092\t0.236\t4\t4\t13\t1\t13\tCUST_15609_PI419289827\tCU995582.p.cg.6\tCU995582\t\tCCTGGAATTTAACAATCCACTCCCCCGGGTTTTTCCCTTTTTAAAAATATAAAAAACAAG\r", "\r\n", "AM862909\tAM862909.p.cg.6\t595\t0\t0\t0\t14\t1\t14\tCUST_4684_PI419289827\tAM862909.p.cg.6\tAM862909\t\tCTACGCTCTACTAATGTCATTTTCAGACATTATCATGACATGTACCAGATGAAATACTAC\r", "\r\n", "CU991229\tCU991229.p.cg.6\t1230\t7.767\t146\t148\t15\t1\t15\tCUST_13060_PI419289827\tCU991229.p.cg.6\tCU991229\tpredicted protein [Trichoplax adhaerens]\tTAGGCATACCCATCTGTATCATGTCTAGTAGCTATTGCCCTTGAATTATTAGGAATTAAA\r", "\r\n", "AM863560\tAM863560.p.cg.6\t562\t11.601\t101\t101\t17\t1\t17\tCUST_4942_PI419289827\tAM863560.p.cg.6\tAM863560\t(sp:Q7ZVC2) Clusterin-associated protein 1 homolog OS=Danio rerio GN=cluap1 PE=2 SV=2\tTAAAAGAAGCAAGAAGACTGGCATCAGAAATAACCACCAAAGGAGCAACTTTATATGATC\r", "\r\n", "AM868645\tAM868645.p.cg.6\t462\t0.279\t2\t2\t18\t1\t18\tCUST_25910_PI419289827\tAM868645.p.cg.6\tAM868645\t\tTGAATACCAAATTGTTGCAATAAAAAATCTGCTACAGAAGAACAACAAGGGTTCTTGTGG\r", "\r\n", "AM856822\tAM856822.p.cg.6\t846\t0\t0\t0\t19\t1\t19\tCUST_2145_PI419289827\tAM856822.p.cg.6\tAM856822\t\tCCTCGTCAAGACCACAGTGATAAACACAACCACAAATAATGTAGGTTATTAAGATTAGAA\r", "\r\n", "FP006184\tFP006184.p.cg.6\t287\t3.599\t16\t16\t20\t1\t20\tCUST_22004_PI419289827\tFP006184.p.cg.6\tFP006184\tHomo sapiens 5.8S ribosomal RNA (LOC100008587), non-coding RNA\tGCTCACTAGTTGACCTAACGGACCATTCTGAATAAAAGATTATCATTTATATTGGACTTC\r", "\r\n", "AM862004\tAM862004.p.cg.6\t808\t10.545\t132\t132\t21\t1\t21\tCUST_28017_PI419289827\tAM862004.p.cg.6\tAM862004\t\tAGCTACGAGTGCTGAATGATGCGAGATTACACAATACATGTGTGTGTCATGGCCGAGTTT\r", "\r\n", "CU998134\tCU998134.p.cg.6\t1001\t49.783\t772\t772\t22\t1\t22\tCUST_17107_PI419289827\tCU998134.p.cg.6\tCU998134\t\tACCCGAAGTCACTCATTTCCAAATTCAAGGGTTTGGAAAAGTTTCAAATGGGTTTTAAAA\r", "\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!python /Applications/q \"SELECT * FROM /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt WHERE c1 like CU995582\"" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "query error: no such column: CU995582\r\n" ] } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"CU995582\" /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "CU995582\tCU995582.p.cg.6\t1092\t0.236\t4\t4\t13\t1\t13\tCUST_15609_PI419289827\tCU995582.p.cg.6\tCU995582\t\tCCTGGAATTTAACAATCCACTCCCCCGGGTTTTTCCCTTTTTAAAAATATAAAAAACAAG\r", "\r\n" ] } ], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -3 /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ID\tSig_No\tGene length\tRPKM\tUnique gene reads\tTotal gene reads\tID\tRow\tCol\tProbeName\tContigName\tGB_ACC\tDescription\tSEQUENCE\r", "\r\n", "CU995582\tCU995582.p.cg.6\t1092\t0.236\t4\t4\t13\t1\t13\tCUST_15609_PI419289827\tCU995582.p.cg.6\tCU995582\t\tCCTGGAATTTAACAATCCACTCCCCCGGGTTTTTCCCTTTTTAAAAATATAAAAAACAAG\r", "\r\n", "AM862909\tAM862909.p.cg.6\t595\t0\t0\t0\t14\t1\t14\tCUST_4684_PI419289827\tAM862909.p.cg.6\tAM862909\t\tCTACGCTCTACTAATGTCATTTTCAGACATTATCATGACATGTACCAGATGAAATACTAC\r", "\r\n" ] } ], "prompt_number": 37 }, { "cell_type": "code", "collapsed": false, "input": [ "!egrep -wi --color 'CF369228|EF219426|EF219427|EF219428|EF219429' /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\u001b[01;31m\u001b[KEF219429\u001b[m\u001b[K\t\u001b[01;31m\u001b[KEF219429\u001b[m\u001b[K.p.cg.6\t2460\t10.758\t45\t410\t12243\t145\t3\tCUST_24587_PI419289827\t\u001b[01;31m\u001b[KEF219429\u001b[m\u001b[K.p.cg.6\t\u001b[01;31m\u001b[KEF219429\u001b[m\u001b[K\thypothetical protein BRAFLDRAFT_118409 [Branchiostoma floridae]\tCAGTGTTTATGGCAGTTTCAGAGGACACTATTGTGTCAACGGAAATACAAAAGATTTTTT\r", "\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\u001b[01;31m\u001b[KEF219426\u001b[m\u001b[K\t\u001b[01;31m\u001b[KEF219426\u001b[m\u001b[K.p.cg.6\t1221\t1.004\t1\t19\t21490\t253\t70\tCUST_24584_PI419289827\t\u001b[01;31m\u001b[KEF219426\u001b[m\u001b[K.p.cg.6\t\u001b[01;31m\u001b[KEF219426\u001b[m\u001b[K\thypothetical protein BRAFLDRAFT_118409 [Branchiostoma floridae]\tTTGATCTTGGGGCTGTTAACAACGTTGACAAAGTGGTCATCTATAACCGGAACGTTCAGG\r", "\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\u001b[01;31m\u001b[KEF219427\u001b[m\u001b[K\t\u001b[01;31m\u001b[KEF219427\u001b[m\u001b[K.p.cg.6\t1641\t15.656\t52\t398\t32629\t384\t74\tCUST_24585_PI419289827\t\u001b[01;31m\u001b[KEF219427\u001b[m\u001b[K.p.cg.6\t\u001b[01;31m\u001b[KEF219427\u001b[m\u001b[K\thypothetical protein BRAFLDRAFT_118409 [Branchiostoma floridae]\tAGGACGTTTTAGGAATGCATTCATACGTGTTGGAGTATCAATAAATAGACTGAGGAAATG\r", "\r\n", "\u001b[01;31m\u001b[KCF369228\u001b[m\u001b[K\t\u001b[01;31m\u001b[KCF369228\u001b[m\u001b[K.p.cg.6\t1088\t926.486\t9709\t15616\t33033\t389\t53\tCUST_24740_PI419289827\t\u001b[01;31m\u001b[KCF369228\u001b[m\u001b[K.p.cg.6\t\u001b[01;31m\u001b[KCF369228\u001b[m\u001b[K\thypothetical protein BRAFLDRAFT_125849 [Branchiostoma floridae]\tCCCAAAATAGAGAATTTTCAAGTATGTTGTACCATTGACAGGGGTAAAAGGGAATGTTAA\r", "\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\u001b[01;31m\u001b[KEF219428\u001b[m\u001b[K\t\u001b[01;31m\u001b[KEF219428\u001b[m\u001b[K.p.cg.6\t2049\t256.783\t773\t8151\t38965\t459\t35\tCUST_24586_PI419289827\t\u001b[01;31m\u001b[KEF219428\u001b[m\u001b[K.p.cg.6\t\u001b[01;31m\u001b[KEF219428\u001b[m\u001b[K\thypothetical protein BRAFLDRAFT_118409 [Branchiostoma floridae]\tGACGTGCAAGTTTTTGGAGGTTAATTAGACTCTGTTAACCAAGAGCATATACTTTGCTTT\r", "\r\n" ] } ], "prompt_number": 35 }, { "cell_type": "code", "collapsed": false, "input": [ "!egrep -wi --color 'CU998852' /Volumes/web/cnidarian/BiRNAseq_GPL11353_v6ref.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\u001b[01;31m\u001b[KCU998852\u001b[m\u001b[K\t\u001b[01;31m\u001b[KCU998852\u001b[m\u001b[K.p.cg.6\t449\t229.304\t1595\t1595\t9555\t113\t35\tCUST_30571_PI419289827\t\u001b[01;31m\u001b[KCU998852\u001b[m\u001b[K.p.cg.6\t\u001b[01;31m\u001b[KCU998852\u001b[m\u001b[K\t(sp:Q9C005) Protein dpy-30 homolog OS=Homo sapiens GN=DPY30 PE=1 SV=1\tCTGTGAACTTGTTACAGTTTTCATGCATTCATCTGTTATTTGTGTCTCGACAGTATCATT\r", "\r\n" ] } ], "prompt_number": 36 }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "BiGo Sperm RNAseq v GPL11353 array" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"SQLShare_-_View_Query_18F591B3.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "heading", "level": 3, "metadata": {}, "source": [ "Supplementary tables from Dheilly et al " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"SQLShare_-_View_Query_18F5948F.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "\"SQLShare_-_View_Query_18F5959E.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "\"SQLShare_-_View_Query_18F5994E.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "--- \n", "\"SQLShare_-_View_Query_18F5996D.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }