deletions | additions       diff --git a/ipynb/RNA-seq-Gene-ID.ipynb b/ipynb/RNA-seq-Gene-ID.ipynb  index 4518162..e47210c 100644  --- a/ipynb/RNA-seq-Gene-ID.ipynb  +++ b/ipynb/RNA-seq-Gene-ID.ipynb 
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{  "cell_type": "code",  "collapsed": false,  "input": [], [  "sqls=\"/Applications/bioinfo/sqlshare-pythonclient/tools/\""  ],  "language": "python",  "metadata": {},  "outputs": [] [],  "prompt_number": 64  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!python {sqls}singleupload.py \\\n",  "-d _blast_sprot _rebuilt.gtf.geneIDend  \\\n", "../analyses/{sp}_sprot_sql.tab "/Users/sr320/data-genomic/tentacle/rebuilt.gtf.geneIDend "  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "processing chunk line 0 to 486015 (0.167377948761 s elapsed)\r\n",  "pushing /Users/sr320/data-genomic/tentacle/rebuilt.gtf.geneIDend...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "parsing 06912255...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "processing chunk line 486015 to 969459 (98.0686910152 s elapsed)\r\n",  "pushing /Users/sr320/data-genomic/tentacle/rebuilt.gtf.geneIDend...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "parsing 149D1ED9...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "processing chunk line 969459 to 1347244 (209.124155998 s elapsed)\r\n",  "pushing /Users/sr320/data-genomic/tentacle/rebuilt.gtf.geneIDend...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "parsing EDC0423B...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "finished _rebuilt.gtf.geneIDend\r\n"  ]  }  ],  "prompt_number": 65  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!python {sqls}singleupload.py \\\n",  "-d _cuffdiffgenes.sorted_by_expression.sig.txt \\\n",  "./data/Cuffdiff2_heat-b-2014-12-20-22-27-15.4/sorted_data/genes.sorted_by_expression.sig.txt"  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "processing chunk line 0 to 1551 (0.000243902206421 s elapsed)\r\n",  "pushing ./data/Cuffdiff2_heat-b-2014-12-20-22-27-15.4/sorted_data/genes.sorted_by_expression.sig.txt...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "parsing 9504F7E0...\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  "finished _cuffdiffgenes.sorted_by_expression.sig.txt\r\n"  ]  }  ],  "prompt_number": 66  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!python {sqls}fetchdata.py \\\n",  "-s \"SELECT Column1, Column2, Column3, Column4, Column5, Column6, Column7, Column8, Column9 \\\n",  "FROM [[email protected]].[_cuffdiffgenes.sorted_by_expression.sig.txt]sig \\\n",  "left join \\\n",  "[[email protected]].[_rebuilt.gtf.geneIDend]id \\\n",  "on \\\n",  "sig.gene_ID=id.Column10\" \\\n",  "-f tsv \\\n",  "-o /Users/sr320/data-genomic/tentacle/diffgene.gtf\n",  "!head /Users/sr320/data-genomic/tentacle/diffgene.gtf  " ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "Column1\tColumn2\tColumn3\tColumn4\tColumn5\tColumn6\tColumn7\tColumn8\tColumn9\r",  "\r\n",  "C17036\tCufflinks\texon\t245\t442\t.\t.\t.\tgene_id XLOC_000059; tss_id \"TSS59\"; oId \"CUFF.56.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000059\"\r",  "\r\n",  "C17036\tCufflinks\tCDS\t245\t442\t.\t.\t.\tgene_id XLOC_000059; tss_id \"TSS59\"; oId \"CUFF.56.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000059\"\r",  "\r\n",  "C18346\tCufflinks\texon\t174\t551\t.\t+\t.\tgene_id CGI_10000009; tss_id \"TSS114\"; nearest_ref \"EKC17950\"; exon_number \"1\"; class_code \"=\"; p_id \"P6\"; gene_name \"CGI_10000009\"; transcript_id \"EKC17950\"\r",  "\r\n",  "C18346\tCufflinks\tCDS\t174\t551\t.\t+\t.\tgene_id CGI_10000009; tss_id \"TSS114\"; nearest_ref \"EKC17950\"; exon_number \"1\"; class_code \"=\"; p_id \"P6\"; gene_name \"CGI_10000009\"; transcript_id \"EKC17950\"\r",  "\r\n",  "C18548\tCufflinks\texon\t1\t33\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18548\tCufflinks\tCDS\t1\t33\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18548\tCufflinks\texon\t300\t629\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"2\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18548\tCufflinks\tCDS\t300\t629\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"2\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18752\tCufflinks\texon\t2\t631\t.\t.\t.\tgene_id XLOC_000133; tss_id \"TSS133\"; oId \"CUFF.125.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000133\"\r",  "\r\n"  ]  }  ],  "prompt_number": 71  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!wc -l /Users/sr320/data-genomic/tentacle/diffgene.gtf "  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  " 122039 /Users/sr320/data-genomic/tentacle/diffgene.gtf\r\n"  ]  }  ],  "prompt_number": 72  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!tail -n +2 /Users/sr320/data-genomic/tentacle/diffgene.gtf > /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf "  ],  "language": "python",  "metadata": {},  "outputs": [],  "prompt_number": 73  },  {  "cell_type": "code",  "collapsed": false,  "input": [],  "language": "python",  "metadata": {},  "outputs": []  }  ],