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  1. {
  2. "cells": [
  3. {
  4. "cell_type": "code",
  5. "execution_count": 3,
  6. "metadata": {
  7. "collapsed": false
  8. },
  9. "outputs": [
  10. {
  11. "name": "stderr",
  12. "output_type": "stream",
  13. "text": [
  14. "Loading required package: gplots\n",
  15. "\n",
  16. "Attaching package: ‘gplots’\n",
  17. "\n",
  18. "The following object is masked from ‘package:stats’:\n",
  19. "\n",
  20. " lowess\n",
  21. "\n",
  22. "Loading required package: parallel\n",
  23. "Loading required package: tools\n",
  24. "Loading required package: gtools\n",
  25. "\n",
  26. "Attaching package: ‘rage’\n",
  27. "\n",
  28. "The following object is masked _by_ ‘.GlobalEnv’:\n",
  29. "\n",
  30. " bed.intersect\n",
  31. "\n"
  32. ]
  33. }
  34. ],
  35. "source": [
  36. "library(rage)\n"
  37. ]
  38. },
  39. {
  40. "cell_type": "code",
  41. "execution_count": 23,
  42. "metadata": {
  43. "collapsed": false
  44. },
  45. "outputs": [],
  46. "source": [
  47. "dl=read.tsv(\"../datalist\")"
  48. ]
  49. },
  50. {
  51. "cell_type": "code",
  52. "execution_count": 24,
  53. "metadata": {
  54. "collapsed": false
  55. },
  56. "outputs": [
  57. {
  58. "data": {
  59. "text/html": [
  60. "<table>\n",
  61. "<thead><tr><th></th><th scope=col>V1</th><th scope=col>V2</th><th scope=col>V3</th></tr></thead>\n",
  62. "<tbody>\n",
  63. "\t<tr><th scope=row>1</th><td>PALTIC</td><td>S</td><td>001_02LRT140414PALTICs_CGATGT.fastq</td></tr>\n",
  64. "\t<tr><th scope=row>2</th><td>PALTIC</td><td>G1</td><td>209_PALTICg.fastq</td></tr>\n",
  65. "\t<tr><th scope=row>3</th><td>PALTWS</td><td>S</td><td>003_05LRT140414PALTWSs_ACAGTG.fastq</td></tr>\n",
  66. "\t<tr><th scope=row>4</th><td>PALTWS</td><td>G1</td><td>004_06LRT140414PALTWSg1_GCCAAT.fastq</td></tr>\n",
  67. "\t<tr><th scope=row>5</th><td>PALUAH</td><td>S</td><td>211_PALUAHs.fastq</td></tr>\n",
  68. "\t<tr><th scope=row>6</th><td>PALUAH</td><td>G1</td><td>210_PALUAHg.fastq</td></tr>\n",
  69. "\t<tr><th scope=row>7</th><td>PALUCR</td><td>S</td><td>007_13LRT140414PALUCRs_AGTCAA.fastq</td></tr>\n",
  70. "\t<tr><th scope=row>8</th><td>PALUCR</td><td>G1</td><td>152_14PALUCRg140422.fastq</td></tr>\n",
  71. "\t<tr><th scope=row>9</th><td>PALXCX</td><td>S</td><td>213_PALXCXs.fastq</td></tr>\n",
  72. "\t<tr><th scope=row>10</th><td>PALXCX</td><td>G1</td><td>212_PALXCXg.fastq</td></tr>\n",
  73. "\t<tr><th scope=row>11</th><td>PAMBWS</td><td>S</td><td>011_18LRT140414PAMBWSs_GTCCGC.fastq</td></tr>\n",
  74. "\t<tr><th scope=row>12</th><td>PAMBWS</td><td>G1</td><td>012_19LRT140414PAMBWSg1_GTGAAA.fastq</td></tr>\n",
  75. "\t<tr><th scope=row>13</th><td>PALFWK</td><td>S</td><td>195_PALFWKs.fastq</td></tr>\n",
  76. "\t<tr><th scope=row>14</th><td>PALFWK</td><td>G1</td><td>194_PALFWKg.fastq</td></tr>\n",
  77. "\t<tr><th scope=row>15</th><td>PALIBN</td><td>S</td><td>198_PALIBNs.fastq</td></tr>\n",
  78. "\t<tr><th scope=row>16</th><td>PALIBN</td><td>G1</td><td>197_PALIBNg.fastq</td></tr>\n",
  79. "\t<tr><th scope=row>17</th><td>PALIYC</td><td>S</td><td>200_PALIYCs.fastq</td></tr>\n",
  80. "\t<tr><th scope=row>18</th><td>PALIYC</td><td>G1</td><td>199_PALIYCg.fastq</td></tr>\n",
  81. "\t<tr><th scope=row>19</th><td>PAMFDX</td><td>S</td><td>228_PAMFDXs.fastq</td></tr>\n",
  82. "\t<tr><th scope=row>20</th><td>PAMFDX</td><td>G1</td><td>216_PAMFDXg.fastq</td></tr>\n",
  83. "\t<tr><th scope=row>21</th><td>PAMHUK</td><td>S</td><td>021_05PAMHUKs120812_ACAGTG.fastq</td></tr>\n",
  84. "\t<tr><th scope=row>22</th><td>PAMHUK</td><td>G1</td><td>217_PAMHUKg.fastq</td></tr>\n",
  85. "\t<tr><th scope=row>23</th><td>PAMVRD</td><td>S</td><td>218_PAMVRDs.fastq</td></tr>\n",
  86. "\t<tr><th scope=row>24</th><td>PAMVRD</td><td>G1</td><td>219_PAMVRDg.fastq</td></tr>\n",
  87. "\t<tr><th scope=row>25</th><td>PAMYIY</td><td>S</td><td>220_PAMYIYs.fastq</td></tr>\n",
  88. "\t<tr><th scope=row>26</th><td>PAMYIY</td><td>G1</td><td>221_PAMYIYg.fastq</td></tr>\n",
  89. "\t<tr><th scope=row>27</th><td>PANAFR</td><td>S</td><td>027_15PANAFRs120812_ATGTCA.fastq</td></tr>\n",
  90. "\t<tr><th scope=row>28</th><td>PANAFR</td><td>G1</td><td>222_PANAFRg.fastq</td></tr>\n",
  91. "\t<tr><th scope=row>29</th><td>PANBUL</td><td>S</td><td>224_PANBULs.fastq</td></tr>\n",
  92. "\t<tr><th scope=row>30</th><td>PANBUL</td><td>G1</td><td>223_PANBULg.fastq</td></tr>\n",
  93. "\t<tr><th scope=row>31</th><td>PAMBWY</td><td>S</td><td>031_02LRT140413_CGATGT.fastq</td></tr>\n",
  94. "\t<tr><th scope=row>32</th><td>PAMBWY</td><td>G1</td><td>032_04LRT140413_TGACCA.fastq</td></tr>\n",
  95. "\t<tr><th scope=row>33</th><td>PAMDRM</td><td>S</td><td>033_05LRT140413_ACAGTG.fastq</td></tr>\n",
  96. "\t<tr><th scope=row>34</th><td>PAMDRM</td><td>G1</td><td>034_06LRT140413_GCCAAT.fastq</td></tr>\n",
  97. "\t<tr><th scope=row>35</th><td>PAMERR</td><td>S</td><td>215_PAMERRs.fastq</td></tr>\n",
  98. "\t<tr><th scope=row>36</th><td>PAMERR</td><td>G1</td><td>214_PAMERRg.fastq</td></tr>\n",
  99. "\t<tr><th scope=row>37</th><td>PALNTB</td><td>S</td><td>202_PALNTBs.fastq</td></tr>\n",
  100. "\t<tr><th scope=row>38</th><td>PALNTB</td><td>G1</td><td>201_PALNTBg.fastq</td></tr>\n",
  101. "\t<tr><th scope=row>39</th><td>PALPHR</td><td>S</td><td>039_15PALPHRs140515_ATGTCA.fastq</td></tr>\n",
  102. "\t<tr><th scope=row>40</th><td>PALPHR</td><td>G1</td><td>203_PALPHRg.fastq</td></tr>\n",
  103. "\t<tr><th scope=row>41</th><td>PALSER</td><td>S</td><td>205_PALSERs.fastq</td></tr>\n",
  104. "\t<tr><th scope=row>42</th><td>PALSER</td><td>G1</td><td>204_PALSERg.fastq</td></tr>\n",
  105. "\t<tr><th scope=row>43</th><td>PANFDP</td><td>S</td><td>045_05PANFDPs141001_ACAGTG.fastq</td></tr>\n",
  106. "\t<tr><th scope=row>44</th><td>PANFDP</td><td>G1</td><td>046_06PANFDPg1401002_GCCAAT.fastq</td></tr>\n",
  107. "\t<tr><th scope=row>45</th><td>PANILL</td><td>S</td><td>047_07PANILLs141001_CAGATC.fastq</td></tr>\n",
  108. "\t<tr><th scope=row>46</th><td>PANILL</td><td>G1</td><td>048_12PANILLg141001_CTTGTA.fastq</td></tr>\n",
  109. "\t<tr><th scope=row>47</th><td>PANLXU</td><td>S</td><td>226_PANLXUs.fastq</td></tr>\n",
  110. "\t<tr><th scope=row>48</th><td>PANLXU</td><td>G1</td><td>225_PANLXUg.fastq</td></tr>\n",
  111. "\t<tr><th scope=row>49</th><td>PALSSJ</td><td>S</td><td>208_PALSSJs.fastq</td></tr>\n",
  112. "\t<tr><th scope=row>50</th><td>PALSSJ</td><td>G1</td><td>207_PALSSJg.fastq</td></tr>\n",
  113. "\t<tr><th scope=row>51</th><td>PAIXGP</td><td>S</td><td>075_PAIXGPs.fastq</td></tr>\n",
  114. "\t<tr><th scope=row>52</th><td>PAIXGP</td><td>G1</td><td>178_PAIXGPg.fastq</td></tr>\n",
  115. "\t<tr><th scope=row>53</th><td>PAIXPH</td><td>S</td><td>180_PAIXPHs.fastq</td></tr>\n",
  116. "\t<tr><th scope=row>54</th><td>PAIXPH</td><td>G1</td><td>179_PAIXPHg.fastq</td></tr>\n",
  117. "\t<tr><th scope=row>55</th><td>PAKHSV</td><td>S</td><td>182_PAKHSVs.fastq</td></tr>\n",
  118. "\t<tr><th scope=row>56</th><td>PAKHSV</td><td>G1</td><td>181_PAKHSVg.fastq</td></tr>\n",
  119. "\t<tr><th scope=row>57</th><td>PAKKMW</td><td>S</td><td>059_10PAKKMWs141002_TAGCTT.fastq</td></tr>\n",
  120. "\t<tr><th scope=row>58</th><td>PAKKMW</td><td>G1</td><td>060_11PAKKMWg141001_GGCTAC.fastq</td></tr>\n",
  121. "\t<tr><th scope=row>59</th><td>PAKUMZ</td><td>S</td><td>184_PAKUMZs.fastq</td></tr>\n",
  122. "\t<tr><th scope=row>60</th><td>PAKUMZ</td><td>G1</td><td>183_PAKUMZg.fastq</td></tr>\n",
  123. "\t<tr><th scope=row>61</th><td>PALAUR</td><td>S</td><td>063_22PALAURs141002_CGTACG.fastq</td></tr>\n",
  124. "\t<tr><th scope=row>62</th><td>PALAUR</td><td>G1</td><td>185_PALAURg.fastq</td></tr>\n",
  125. "\t<tr><th scope=row>63</th><td>PALBFB</td><td>S</td><td>187_PALBFBs.fastq</td></tr>\n",
  126. "\t<tr><th scope=row>64</th><td>PALBFB</td><td>G1</td><td>186_PALBFBg.fastq</td></tr>\n",
  127. "\t<tr><th scope=row>65</th><td>PALBLM</td><td>S</td><td>189_PALBLMs.fastq</td></tr>\n",
  128. "\t<tr><th scope=row>66</th><td>PALBLM</td><td>G1</td><td>188_PALBLMg.fastq</td></tr>\n",
  129. "\t<tr><th scope=row>67</th><td>PAKGHN</td><td>S</td><td>122_05PAKGHNs150318_ACAGTG.fastq</td></tr>\n",
  130. "\t<tr><th scope=row>68</th><td>PAKGHN</td><td>G1</td><td>123_06PAKGHNg150318_GCCAAT.fastq</td></tr>\n",
  131. "\t<tr><th scope=row>69</th><td>PAKFNI</td><td>S</td><td>140_02PAKFNIs150407_CGATGT.fastq</td></tr>\n",
  132. "\t<tr><th scope=row>70</th><td>PAKFNI</td><td>G1</td><td>141_04PAKFNIg150407_TGACCA.fastq</td></tr>\n",
  133. "\t<tr><th scope=row>71</th><td>PAKGUA</td><td>S</td><td>128_15PAKGUAs150318_ATGTCA.fastq</td></tr>\n",
  134. "\t<tr><th scope=row>72</th><td>PAKGUA</td><td>G1</td><td>129_16PAKGUAg150318_CCGTCC.fastq</td></tr>\n",
  135. "\t<tr><th scope=row>73</th><td>PAKHJJ</td><td>S</td><td>130_18PAKHJJs150318_GTCCGC.fastq</td></tr>\n",
  136. "\t<tr><th scope=row>74</th><td>PAKHJJ</td><td>G1</td><td>131_19PAKHJJg150318_GTGAAA.fastq</td></tr>\n",
  137. "\t<tr><th scope=row>75</th><td>PAKHSB</td><td>S</td><td>126_13PAKHSBs150318_AGTCAA.fastq</td></tr>\n",
  138. "\t<tr><th scope=row>76</th><td>PAKHSB</td><td>G1</td><td>127_14PAKHSBg150318_AGTTCC.fastq</td></tr>\n",
  139. "\t<tr><th scope=row>77</th><td>PAKHSH</td><td>S</td><td>124_07PAKHSHs150318_CAGATC.fastq</td></tr>\n",
  140. "\t<tr><th scope=row>78</th><td>PAKHSH</td><td>G1</td><td>125_12PAKHSHg150318_CTTGTA.fastq</td></tr>\n",
  141. "\t<tr><th scope=row>79</th><td>PAKHUL</td><td>S</td><td>142_05PAKHULs150407_ACAGTG.fastq</td></tr>\n",
  142. "\t<tr><th scope=row>80</th><td>PAKHUL</td><td>G1</td><td>143_06PAKHULg150407_GCCAAT.fastq</td></tr>\n",
  143. "\t<tr><th scope=row>81</th><td>PALFGP</td><td>S</td><td>144_07PALFGPs150407_CAGATC.fastq</td></tr>\n",
  144. "\t<tr><th scope=row>82</th><td>PALFGP</td><td>G1</td><td>145_12PALFGPg150407_CTTGTA.fastq</td></tr>\n",
  145. "\t<tr><th scope=row>83</th><td>PALJVL</td><td>S</td><td>148_15PALJVLs150407_ATGTCA.fastq</td></tr>\n",
  146. "\t<tr><th scope=row>84</th><td>PALJVL</td><td>G1</td><td>149_16PALJVLg150407_CCGTCC.fastq</td></tr>\n",
  147. "\t<tr><th scope=row>85</th><td>PALKYT</td><td>S</td><td>132_01PALKYTs150318_ATCACG.fastq</td></tr>\n",
  148. "\t<tr><th scope=row>86</th><td>PALKYT</td><td>G1</td><td>133_03PALKYTg150318_TTAGGC.fastq</td></tr>\n",
  149. "\t<tr><th scope=row>87</th><td>PALMSX</td><td>S</td><td>134_08PALMSXs150318_ACTTGA.fastq</td></tr>\n",
  150. "\t<tr><th scope=row>88</th><td>PALMSX</td><td>G1</td><td>135_09PALMSXg150318_GATCAG.fastq</td></tr>\n",
  151. "\t<tr><th scope=row>89</th><td>PALNLD</td><td>S</td><td>150_18PALNLDs150407_GTCCGC.fastq</td></tr>\n",
  152. "\t<tr><th scope=row>90</th><td>PALNLD</td><td>G1</td><td>151_19PALNLDg150407_GTGAAA.fastq</td></tr>\n",
  153. "\t<tr><th scope=row>91</th><td>PALNUA</td><td>S</td><td>136_10PALNUAs150318_TAGCTT.fastq</td></tr>\n",
  154. "\t<tr><th scope=row>92</th><td>PALNUA</td><td>G1</td><td>137_11PALNUAg150318_GGCTAC.fastq</td></tr>\n",
  155. "\t<tr><th scope=row>93</th><td>PALPEM</td><td>S</td><td>138_20PALPEMs150318_GTGGCC.fastq</td></tr>\n",
  156. "\t<tr><th scope=row>94</th><td>PALPEM</td><td>G1</td><td>139_21PALPEMg150318_GTTTCG.fastq</td></tr>\n",
  157. "\t<tr><th scope=row>95</th><td>PAIXFK</td><td>S</td><td>120_02PAIXFKs150318_CGATGT.fastq</td></tr>\n",
  158. "\t<tr><th scope=row>96</th><td>PAIXFK</td><td>G1</td><td>177_PAIXFKg.fastq</td></tr>\n",
  159. "\t<tr><th scope=row>97</th><td>PALDNV</td><td>S</td><td>191_PALDNVs.fastq</td></tr>\n",
  160. "\t<tr><th scope=row>98</th><td>PALDNV</td><td>G1</td><td>190_PALDNAg.fastq</td></tr>\n",
  161. "\t<tr><th scope=row>99</th><td>PALSJC</td><td>S</td><td>206_PALSICs.fastq</td></tr>\n",
  162. "\t<tr><th scope=row>100</th><td>PALSJC</td><td>G1</td><td>227_PALSJCg.fastq</td></tr>\n",
  163. "\t<tr><th scope=row>101</th><td>PALEZS</td><td>S</td><td>193_PALEZSs.fastq</td></tr>\n",
  164. "\t<tr><th scope=row>102</th><td>PALEZS</td><td>G1</td><td>192_PALEZSg.fastq</td></tr>\n",
  165. "\t<tr><th scope=row>103</th><td>PALHPA</td><td>S</td><td>196_PALHPAs.fastq</td></tr>\n",
  166. "\t<tr><th scope=row>104</th><td>PALHPA</td><td>G1</td><td>147_14PALHPAg150407_AGTTCC.fastq</td></tr>\n",
  167. "</tbody>\n",
  168. "</table>\n"
  169. ],
  170. "text/latex": [
  171. "\\begin{tabular}{r|lll}\n",
  172. " & V1 & V2 & V3\\\\\n",
  173. "\\hline\n",
  174. "\t1 & PALTIC & S & 001_02LRT140414PALTICs_CGATGT.fastq\\\\\n",
  175. "\t2 & PALTIC & G1 & 209_PALTICg.fastq\\\\\n",
  176. "\t3 & PALTWS & S & 003_05LRT140414PALTWSs_ACAGTG.fastq\\\\\n",
  177. "\t4 & PALTWS & G1 & 004_06LRT140414PALTWSg1_GCCAAT.fastq\\\\\n",
  178. "\t5 & PALUAH & S & 211_PALUAHs.fastq\\\\\n",
  179. "\t6 & PALUAH & G1 & 210_PALUAHg.fastq\\\\\n",
  180. "\t7 & PALUCR & S & 007_13LRT140414PALUCRs_AGTCAA.fastq\\\\\n",
  181. "\t8 & PALUCR & G1 & 152_14PALUCRg140422.fastq\\\\\n",
  182. "\t9 & PALXCX & S & 213_PALXCXs.fastq\\\\\n",
  183. "\t10 & PALXCX & G1 & 212_PALXCXg.fastq\\\\\n",
  184. "\t11 & PAMBWS & S & 011_18LRT140414PAMBWSs_GTCCGC.fastq\\\\\n",
  185. "\t12 & PAMBWS & G1 & 012_19LRT140414PAMBWSg1_GTGAAA.fastq\\\\\n",
  186. "\t13 & PALFWK & S & 195_PALFWKs.fastq\\\\\n",
  187. "\t14 & PALFWK & G1 & 194_PALFWKg.fastq\\\\\n",
  188. "\t15 & PALIBN & S & 198_PALIBNs.fastq\\\\\n",
  189. "\t16 & PALIBN & G1 & 197_PALIBNg.fastq\\\\\n",
  190. "\t17 & PALIYC & S & 200_PALIYCs.fastq\\\\\n",
  191. "\t18 & PALIYC & G1 & 199_PALIYCg.fastq\\\\\n",
  192. "\t19 & PAMFDX & S & 228_PAMFDXs.fastq\\\\\n",
  193. "\t20 & PAMFDX & G1 & 216_PAMFDXg.fastq\\\\\n",
  194. "\t21 & PAMHUK & S & 021_05PAMHUKs120812_ACAGTG.fastq\\\\\n",
  195. "\t22 & PAMHUK & G1 & 217_PAMHUKg.fastq\\\\\n",
  196. "\t23 & PAMVRD & S & 218_PAMVRDs.fastq\\\\\n",
  197. "\t24 & PAMVRD & G1 & 219_PAMVRDg.fastq\\\\\n",
  198. "\t25 & PAMYIY & S & 220_PAMYIYs.fastq\\\\\n",
  199. "\t26 & PAMYIY & G1 & 221_PAMYIYg.fastq\\\\\n",
  200. "\t27 & PANAFR & S & 027_15PANAFRs120812_ATGTCA.fastq\\\\\n",
  201. "\t28 & PANAFR & G1 & 222_PANAFRg.fastq\\\\\n",
  202. "\t29 & PANBUL & S & 224_PANBULs.fastq\\\\\n",
  203. "\t30 & PANBUL & G1 & 223_PANBULg.fastq\\\\\n",
  204. "\t31 & PAMBWY & S & 031_02LRT140413_CGATGT.fastq\\\\\n",
  205. "\t32 & PAMBWY & G1 & 032_04LRT140413_TGACCA.fastq\\\\\n",
  206. "\t33 & PAMDRM & S & 033_05LRT140413_ACAGTG.fastq\\\\\n",
  207. "\t34 & PAMDRM & G1 & 034_06LRT140413_GCCAAT.fastq\\\\\n",
  208. "\t35 & PAMERR & S & 215_PAMERRs.fastq\\\\\n",
  209. "\t36 & PAMERR & G1 & 214_PAMERRg.fastq\\\\\n",
  210. "\t37 & PALNTB & S & 202_PALNTBs.fastq\\\\\n",
  211. "\t38 & PALNTB & G1 & 201_PALNTBg.fastq\\\\\n",
  212. "\t39 & PALPHR & S & 039_15PALPHRs140515_ATGTCA.fastq\\\\\n",
  213. "\t40 & PALPHR & G1 & 203_PALPHRg.fastq\\\\\n",
  214. "\t41 & PALSER & S & 205_PALSERs.fastq\\\\\n",
  215. "\t42 & PALSER & G1 & 204_PALSERg.fastq\\\\\n",
  216. "\t43 & PANFDP & S & 045_05PANFDPs141001_ACAGTG.fastq\\\\\n",
  217. "\t44 & PANFDP & G1 & 046_06PANFDPg1401002_GCCAAT.fastq\\\\\n",
  218. "\t45 & PANILL & S & 047_07PANILLs141001_CAGATC.fastq\\\\\n",
  219. "\t46 & PANILL & G1 & 048_12PANILLg141001_CTTGTA.fastq\\\\\n",
  220. "\t47 & PANLXU & S & 226_PANLXUs.fastq\\\\\n",
  221. "\t48 & PANLXU & G1 & 225_PANLXUg.fastq\\\\\n",
  222. "\t49 & PALSSJ & S & 208_PALSSJs.fastq\\\\\n",
  223. "\t50 & PALSSJ & G1 & 207_PALSSJg.fastq\\\\\n",
  224. "\t51 & PAIXGP & S & 075_PAIXGPs.fastq\\\\\n",
  225. "\t52 & PAIXGP & G1 & 178_PAIXGPg.fastq\\\\\n",
  226. "\t53 & PAIXPH & S & 180_PAIXPHs.fastq\\\\\n",
  227. "\t54 & PAIXPH & G1 & 179_PAIXPHg.fastq\\\\\n",
  228. "\t55 & PAKHSV & S & 182_PAKHSVs.fastq\\\\\n",
  229. "\t56 & PAKHSV & G1 & 181_PAKHSVg.fastq\\\\\n",
  230. "\t57 & PAKKMW & S & 059_10PAKKMWs141002_TAGCTT.fastq\\\\\n",
  231. "\t58 & PAKKMW & G1 & 060_11PAKKMWg141001_GGCTAC.fastq\\\\\n",
  232. "\t59 & PAKUMZ & S & 184_PAKUMZs.fastq\\\\\n",
  233. "\t60 & PAKUMZ & G1 & 183_PAKUMZg.fastq\\\\\n",
  234. "\t61 & PALAUR & S & 063_22PALAURs141002_CGTACG.fastq\\\\\n",
  235. "\t62 & PALAUR & G1 & 185_PALAURg.fastq\\\\\n",
  236. "\t63 & PALBFB & S & 187_PALBFBs.fastq\\\\\n",
  237. "\t64 & PALBFB & G1 & 186_PALBFBg.fastq\\\\\n",
  238. "\t65 & PALBLM & S & 189_PALBLMs.fastq\\\\\n",
  239. "\t66 & PALBLM & G1 & 188_PALBLMg.fastq\\\\\n",
  240. "\t67 & PAKGHN & S & 122_05PAKGHNs150318_ACAGTG.fastq\\\\\n",
  241. "\t68 & PAKGHN & G1 & 123_06PAKGHNg150318_GCCAAT.fastq\\\\\n",
  242. "\t69 & PAKFNI & S & 140_02PAKFNIs150407_CGATGT.fastq\\\\\n",
  243. "\t70 & PAKFNI & G1 & 141_04PAKFNIg150407_TGACCA.fastq\\\\\n",
  244. "\t71 & PAKGUA & S & 128_15PAKGUAs150318_ATGTCA.fastq\\\\\n",
  245. "\t72 & PAKGUA & G1 & 129_16PAKGUAg150318_CCGTCC.fastq\\\\\n",
  246. "\t73 & PAKHJJ & S & 130_18PAKHJJs150318_GTCCGC.fastq\\\\\n",
  247. "\t74 & PAKHJJ & G1 & 131_19PAKHJJg150318_GTGAAA.fastq\\\\\n",
  248. "\t75 & PAKHSB & S & 126_13PAKHSBs150318_AGTCAA.fastq\\\\\n",
  249. "\t76 & PAKHSB & G1 & 127_14PAKHSBg150318_AGTTCC.fastq\\\\\n",
  250. "\t77 & PAKHSH & S & 124_07PAKHSHs150318_CAGATC.fastq\\\\\n",
  251. "\t78 & PAKHSH & G1 & 125_12PAKHSHg150318_CTTGTA.fastq\\\\\n",
  252. "\t79 & PAKHUL & S & 142_05PAKHULs150407_ACAGTG.fastq\\\\\n",
  253. "\t80 & PAKHUL & G1 & 143_06PAKHULg150407_GCCAAT.fastq\\\\\n",
  254. "\t81 & PALFGP & S & 144_07PALFGPs150407_CAGATC.fastq\\\\\n",
  255. "\t82 & PALFGP & G1 & 145_12PALFGPg150407_CTTGTA.fastq\\\\\n",
  256. "\t83 & PALJVL & S & 148_15PALJVLs150407_ATGTCA.fastq\\\\\n",
  257. "\t84 & PALJVL & G1 & 149_16PALJVLg150407_CCGTCC.fastq\\\\\n",
  258. "\t85 & PALKYT & S & 132_01PALKYTs150318_ATCACG.fastq\\\\\n",
  259. "\t86 & PALKYT & G1 & 133_03PALKYTg150318_TTAGGC.fastq\\\\\n",
  260. "\t87 & PALMSX & S & 134_08PALMSXs150318_ACTTGA.fastq\\\\\n",
  261. "\t88 & PALMSX & G1 & 135_09PALMSXg150318_GATCAG.fastq\\\\\n",
  262. "\t89 & PALNLD & S & 150_18PALNLDs150407_GTCCGC.fastq\\\\\n",
  263. "\t90 & PALNLD & G1 & 151_19PALNLDg150407_GTGAAA.fastq\\\\\n",
  264. "\t91 & PALNUA & S & 136_10PALNUAs150318_TAGCTT.fastq\\\\\n",
  265. "\t92 & PALNUA & G1 & 137_11PALNUAg150318_GGCTAC.fastq\\\\\n",
  266. "\t93 & PALPEM & S & 138_20PALPEMs150318_GTGGCC.fastq\\\\\n",
  267. "\t94 & PALPEM & G1 & 139_21PALPEMg150318_GTTTCG.fastq\\\\\n",
  268. "\t95 & PAIXFK & S & 120_02PAIXFKs150318_CGATGT.fastq\\\\\n",
  269. "\t96 & PAIXFK & G1 & 177_PAIXFKg.fastq\\\\\n",
  270. "\t97 & PALDNV & S & 191_PALDNVs.fastq\\\\\n",
  271. "\t98 & PALDNV & G1 & 190_PALDNAg.fastq\\\\\n",
  272. "\t99 & PALSJC & S & 206_PALSICs.fastq\\\\\n",
  273. "\t100 & PALSJC & G1 & 227_PALSJCg.fastq\\\\\n",
  274. "\t101 & PALEZS & S & 193_PALEZSs.fastq\\\\\n",
  275. "\t102 & PALEZS & G1 & 192_PALEZSg.fastq\\\\\n",
  276. "\t103 & PALHPA & S & 196_PALHPAs.fastq\\\\\n",
  277. "\t104 & PALHPA & G1 & 147_14PALHPAg150407_AGTTCC.fastq\\\\\n",
  278. "\\end{tabular}\n"
  279. ],
  280. "text/plain": [
  281. " V1 V2 V3\n",
  282. "1 PALTIC S 001_02LRT140414PALTICs_CGATGT.fastq\n",
  283. "2 PALTIC G1 209_PALTICg.fastq\n",
  284. "3 PALTWS S 003_05LRT140414PALTWSs_ACAGTG.fastq\n",
  285. "4 PALTWS G1 004_06LRT140414PALTWSg1_GCCAAT.fastq\n",
  286. "5 PALUAH S 211_PALUAHs.fastq\n",
  287. "6 PALUAH G1 210_PALUAHg.fastq\n",
  288. "7 PALUCR S 007_13LRT140414PALUCRs_AGTCAA.fastq\n",
  289. "8 PALUCR G1 152_14PALUCRg140422.fastq\n",
  290. "9 PALXCX S 213_PALXCXs.fastq\n",
  291. "10 PALXCX G1 212_PALXCXg.fastq\n",
  292. "11 PAMBWS S 011_18LRT140414PAMBWSs_GTCCGC.fastq\n",
  293. "12 PAMBWS G1 012_19LRT140414PAMBWSg1_GTGAAA.fastq\n",
  294. "13 PALFWK S 195_PALFWKs.fastq\n",
  295. "14 PALFWK G1 194_PALFWKg.fastq\n",
  296. "15 PALIBN S 198_PALIBNs.fastq\n",
  297. "16 PALIBN G1 197_PALIBNg.fastq\n",
  298. "17 PALIYC S 200_PALIYCs.fastq\n",
  299. "18 PALIYC G1 199_PALIYCg.fastq\n",
  300. "19 PAMFDX S 228_PAMFDXs.fastq\n",
  301. "20 PAMFDX G1 216_PAMFDXg.fastq\n",
  302. "21 PAMHUK S 021_05PAMHUKs120812_ACAGTG.fastq\n",
  303. "22 PAMHUK G1 217_PAMHUKg.fastq\n",
  304. "23 PAMVRD S 218_PAMVRDs.fastq\n",
  305. "24 PAMVRD G1 219_PAMVRDg.fastq\n",
  306. "25 PAMYIY S 220_PAMYIYs.fastq\n",
  307. "26 PAMYIY G1 221_PAMYIYg.fastq\n",
  308. "27 PANAFR S 027_15PANAFRs120812_ATGTCA.fastq\n",
  309. "28 PANAFR G1 222_PANAFRg.fastq\n",
  310. "29 PANBUL S 224_PANBULs.fastq\n",
  311. "30 PANBUL G1 223_PANBULg.fastq\n",
  312. "31 PAMBWY S 031_02LRT140413_CGATGT.fastq\n",
  313. "32 PAMBWY G1 032_04LRT140413_TGACCA.fastq\n",
  314. "33 PAMDRM S 033_05LRT140413_ACAGTG.fastq\n",
  315. "34 PAMDRM G1 034_06LRT140413_GCCAAT.fastq\n",
  316. "35 PAMERR S 215_PAMERRs.fastq\n",
  317. "36 PAMERR G1 214_PAMERRg.fastq\n",
  318. "37 PALNTB S 202_PALNTBs.fastq\n",
  319. "38 PALNTB G1 201_PALNTBg.fastq\n",
  320. "39 PALPHR S 039_15PALPHRs140515_ATGTCA.fastq\n",
  321. "40 PALPHR G1 203_PALPHRg.fastq\n",
  322. "41 PALSER S 205_PALSERs.fastq\n",
  323. "42 PALSER G1 204_PALSERg.fastq\n",
  324. "43 PANFDP S 045_05PANFDPs141001_ACAGTG.fastq\n",
  325. "44 PANFDP G1 046_06PANFDPg1401002_GCCAAT.fastq\n",
  326. "45 PANILL S 047_07PANILLs141001_CAGATC.fastq\n",
  327. "46 PANILL G1 048_12PANILLg141001_CTTGTA.fastq\n",
  328. "47 PANLXU S 226_PANLXUs.fastq\n",
  329. "48 PANLXU G1 225_PANLXUg.fastq\n",
  330. "49 PALSSJ S 208_PALSSJs.fastq\n",
  331. "50 PALSSJ G1 207_PALSSJg.fastq\n",
  332. "51 PAIXGP S 075_PAIXGPs.fastq\n",
  333. "52 PAIXGP G1 178_PAIXGPg.fastq\n",
  334. "53 PAIXPH S 180_PAIXPHs.fastq\n",
  335. "54 PAIXPH G1 179_PAIXPHg.fastq\n",
  336. "55 PAKHSV S 182_PAKHSVs.fastq\n",
  337. "56 PAKHSV G1 181_PAKHSVg.fastq\n",
  338. "57 PAKKMW S 059_10PAKKMWs141002_TAGCTT.fastq\n",
  339. "58 PAKKMW G1 060_11PAKKMWg141001_GGCTAC.fastq\n",
  340. "59 PAKUMZ S 184_PAKUMZs.fastq\n",
  341. "60 PAKUMZ G1 183_PAKUMZg.fastq\n",
  342. "61 PALAUR S 063_22PALAURs141002_CGTACG.fastq\n",
  343. "62 PALAUR G1 185_PALAURg.fastq\n",
  344. "63 PALBFB S 187_PALBFBs.fastq\n",
  345. "64 PALBFB G1 186_PALBFBg.fastq\n",
  346. "65 PALBLM S 189_PALBLMs.fastq\n",
  347. "66 PALBLM G1 188_PALBLMg.fastq\n",
  348. "67 PAKGHN S 122_05PAKGHNs150318_ACAGTG.fastq\n",
  349. "68 PAKGHN G1 123_06PAKGHNg150318_GCCAAT.fastq\n",
  350. "69 PAKFNI S 140_02PAKFNIs150407_CGATGT.fastq\n",
  351. "70 PAKFNI G1 141_04PAKFNIg150407_TGACCA.fastq\n",
  352. "71 PAKGUA S 128_15PAKGUAs150318_ATGTCA.fastq\n",
  353. "72 PAKGUA G1 129_16PAKGUAg150318_CCGTCC.fastq\n",
  354. "73 PAKHJJ S 130_18PAKHJJs150318_GTCCGC.fastq\n",
  355. "74 PAKHJJ G1 131_19PAKHJJg150318_GTGAAA.fastq\n",
  356. "75 PAKHSB S 126_13PAKHSBs150318_AGTCAA.fastq\n",
  357. "76 PAKHSB G1 127_14PAKHSBg150318_AGTTCC.fastq\n",
  358. "77 PAKHSH S 124_07PAKHSHs150318_CAGATC.fastq\n",
  359. "78 PAKHSH G1 125_12PAKHSHg150318_CTTGTA.fastq\n",
  360. "79 PAKHUL S 142_05PAKHULs150407_ACAGTG.fastq\n",
  361. "80 PAKHUL G1 143_06PAKHULg150407_GCCAAT.fastq\n",
  362. "81 PALFGP S 144_07PALFGPs150407_CAGATC.fastq\n",
  363. "82 PALFGP G1 145_12PALFGPg150407_CTTGTA.fastq\n",
  364. "83 PALJVL S 148_15PALJVLs150407_ATGTCA.fastq\n",
  365. "84 PALJVL G1 149_16PALJVLg150407_CCGTCC.fastq\n",
  366. "85 PALKYT S 132_01PALKYTs150318_ATCACG.fastq\n",
  367. "86 PALKYT G1 133_03PALKYTg150318_TTAGGC.fastq\n",
  368. "87 PALMSX S 134_08PALMSXs150318_ACTTGA.fastq\n",
  369. "88 PALMSX G1 135_09PALMSXg150318_GATCAG.fastq\n",
  370. "89 PALNLD S 150_18PALNLDs150407_GTCCGC.fastq\n",
  371. "90 PALNLD G1 151_19PALNLDg150407_GTGAAA.fastq\n",
  372. "91 PALNUA S 136_10PALNUAs150318_TAGCTT.fastq\n",
  373. "92 PALNUA G1 137_11PALNUAg150318_GGCTAC.fastq\n",
  374. "93 PALPEM S 138_20PALPEMs150318_GTGGCC.fastq\n",
  375. "94 PALPEM G1 139_21PALPEMg150318_GTTTCG.fastq\n",
  376. "95 PAIXFK S 120_02PAIXFKs150318_CGATGT.fastq\n",
  377. "96 PAIXFK G1 177_PAIXFKg.fastq\n",
  378. "97 PALDNV S 191_PALDNVs.fastq\n",
  379. "98 PALDNV G1 190_PALDNAg.fastq\n",
  380. "99 PALSJC S 206_PALSICs.fastq\n",
  381. "100 PALSJC G1 227_PALSJCg.fastq\n",
  382. "101 PALEZS S 193_PALEZSs.fastq\n",
  383. "102 PALEZS G1 192_PALEZSg.fastq\n",
  384. "103 PALHPA S 196_PALHPAs.fastq\n",
  385. "104 PALHPA G1 147_14PALHPAg150407_AGTTCC.fastq"
  386. ]
  387. },
  388. "execution_count": 24,
  389. "metadata": {},
  390. "output_type": "execute_result"
  391. }
  392. ],
  393. "source": [
  394. "dl"
  395. ]
  396. },
  397. {
  398. "cell_type": "code",
  399. "execution_count": 25,
  400. "metadata": {
  401. "collapsed": false
  402. },
  403. "outputs": [
  404. {
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  627. "5. TRUE\n",
  628. "6. TRUE\n",
  629. "7. TRUE\n",
  630. "8. TRUE\n",
  631. "9. TRUE\n",
  632. "10. TRUE\n",
  633. "11. TRUE\n",
  634. "12. TRUE\n",
  635. "13. TRUE\n",
  636. "14. TRUE\n",
  637. "15. TRUE\n",
  638. "16. TRUE\n",
  639. "17. TRUE\n",
  640. "18. TRUE\n",
  641. "19. TRUE\n",
  642. "20. TRUE\n",
  643. "21. TRUE\n",
  644. "22. TRUE\n",
  645. "23. TRUE\n",
  646. "24. TRUE\n",
  647. "25. TRUE\n",
  648. "26. TRUE\n",
  649. "27. TRUE\n",
  650. "28. TRUE\n",
  651. "29. TRUE\n",
  652. "30. TRUE\n",
  653. "31. TRUE\n",
  654. "32. TRUE\n",
  655. "33. TRUE\n",
  656. "34. TRUE\n",
  657. "35. TRUE\n",
  658. "36. TRUE\n",
  659. "37. TRUE\n",
  660. "38. TRUE\n",
  661. "39. TRUE\n",
  662. "40. TRUE\n",
  663. "41. TRUE\n",
  664. "42. TRUE\n",
  665. "43. TRUE\n",
  666. "44. TRUE\n",
  667. "45. TRUE\n",
  668. "46. TRUE\n",
  669. "47. TRUE\n",
  670. "48. TRUE\n",
  671. "49. TRUE\n",
  672. "50. TRUE\n",
  673. "51. TRUE\n",
  674. "52. TRUE\n",
  675. "53. TRUE\n",
  676. "54. TRUE\n",
  677. "55. TRUE\n",
  678. "56. TRUE\n",
  679. "57. TRUE\n",
  680. "58. TRUE\n",
  681. "59. TRUE\n",
  682. "60. TRUE\n",
  683. "61. TRUE\n",
  684. "62. TRUE\n",
  685. "63. TRUE\n",
  686. "64. TRUE\n",
  687. "65. TRUE\n",
  688. "66. TRUE\n",
  689. "67. TRUE\n",
  690. "68. TRUE\n",
  691. "69. TRUE\n",
  692. "70. TRUE\n",
  693. "71. TRUE\n",
  694. "72. TRUE\n",
  695. "73. TRUE\n",
  696. "74. TRUE\n",
  697. "75. TRUE\n",
  698. "76. TRUE\n",
  699. "77. TRUE\n",
  700. "78. TRUE\n",
  701. "79. TRUE\n",
  702. "80. TRUE\n",
  703. "81. TRUE\n",
  704. "82. TRUE\n",
  705. "83. TRUE\n",
  706. "84. TRUE\n",
  707. "85. TRUE\n",
  708. "86. TRUE\n",
  709. "87. TRUE\n",
  710. "88. TRUE\n",
  711. "89. TRUE\n",
  712. "90. TRUE\n",
  713. "91. TRUE\n",
  714. "92. TRUE\n",
  715. "93. TRUE\n",
  716. "94. TRUE\n",
  717. "95. TRUE\n",
  718. "96. TRUE\n",
  719. "97. TRUE\n",
  720. "98. TRUE\n",
  721. "99. TRUE\n",
  722. "100. TRUE\n",
  723. "101. TRUE\n",
  724. "102. TRUE\n",
  725. "103. TRUE\n",
  726. "104. TRUE\n",
  727. "\n",
  728. "\n"
  729. ],
  730. "text/plain": [
  731. " [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE\n",
  732. " [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE\n",
  733. " [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE\n",
  734. " [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE\n",
  735. " [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE\n",
  736. " [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE\n",
  737. " [91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE"
  738. ]
  739. },
  740. "execution_count": 25,
  741. "metadata": {},
  742. "output_type": "execute_result"
  743. }
  744. ],
  745. "source": [
  746. "file.exists(dl$V3)"
  747. ]
  748. },
  749. {
  750. "cell_type": "code",
  751. "execution_count": 26,
  752. "metadata": {
  753. "collapsed": true
  754. },
  755. "outputs": [],
  756. "source": [
  757. "dl$V4=paste0(dl$V1,\"_\",dl$V2,\".fastq\")"
  758. ]
  759. },
  760. {
  761. "cell_type": "code",
  762. "execution_count": 27,
  763. "metadata": {
  764. "collapsed": false
  765. },
  766. "outputs": [
  767. {
  768. "data": {
  769. "text/html": [
  770. "<table>\n",
  771. "<thead><tr><th></th><th scope=col>V1</th><th scope=col>V2</th><th scope=col>V3</th><th scope=col>V4</th></tr></thead>\n",
  772. "<tbody>\n",
  773. "\t<tr><th scope=row>1</th><td>PALTIC</td><td>S</td><td>001_02LRT140414PALTICs_CGATGT.fastq</td><td>PALTIC_S.fastq</td></tr>\n",
  774. "\t<tr><th scope=row>2</th><td>PALTIC</td><td>G1</td><td>209_PALTICg.fastq</td><td>PALTIC_G1.fastq</td></tr>\n",
  775. "\t<tr><th scope=row>3</th><td>PALTWS</td><td>S</td><td>003_05LRT140414PALTWSs_ACAGTG.fastq</td><td>PALTWS_S.fastq</td></tr>\n",
  776. "\t<tr><th scope=row>4</th><td>PALTWS</td><td>G1</td><td>004_06LRT140414PALTWSg1_GCCAAT.fastq</td><td>PALTWS_G1.fastq</td></tr>\n",
  777. "\t<tr><th scope=row>5</th><td>PALUAH</td><td>S</td><td>211_PALUAHs.fastq</td><td>PALUAH_S.fastq</td></tr>\n",
  778. "\t<tr><th scope=row>6</th><td>PALUAH</td><td>G1</td><td>210_PALUAHg.fastq</td><td>PALUAH_G1.fastq</td></tr>\n",
  779. "</tbody>\n",
  780. "</table>\n"
  781. ],
  782. "text/latex": [
  783. "\\begin{tabular}{r|llll}\n",
  784. " & V1 & V2 & V3 & V4\\\\\n",
  785. "\\hline\n",
  786. "\t1 & PALTIC & S & 001_02LRT140414PALTICs_CGATGT.fastq & PALTIC_S.fastq\\\\\n",
  787. "\t2 & PALTIC & G1 & 209_PALTICg.fastq & PALTIC_G1.fastq\\\\\n",
  788. "\t3 & PALTWS & S & 003_05LRT140414PALTWSs_ACAGTG.fastq & PALTWS_S.fastq\\\\\n",
  789. "\t4 & PALTWS & G1 & 004_06LRT140414PALTWSg1_GCCAAT.fastq & PALTWS_G1.fastq\\\\\n",
  790. "\t5 & PALUAH & S & 211_PALUAHs.fastq & PALUAH_S.fastq\\\\\n",
  791. "\t6 & PALUAH & G1 & 210_PALUAHg.fastq & PALUAH_G1.fastq\\\\\n",
  792. "\\end{tabular}\n"
  793. ],
  794. "text/plain": [
  795. " V1 V2 V3 V4\n",
  796. "1 PALTIC S 001_02LRT140414PALTICs_CGATGT.fastq PALTIC_S.fastq\n",
  797. "2 PALTIC G1 209_PALTICg.fastq PALTIC_G1.fastq\n",
  798. "3 PALTWS S 003_05LRT140414PALTWSs_ACAGTG.fastq PALTWS_S.fastq\n",
  799. "4 PALTWS G1 004_06LRT140414PALTWSg1_GCCAAT.fastq PALTWS_G1.fastq\n",
  800. "5 PALUAH S 211_PALUAHs.fastq PALUAH_S.fastq\n",
  801. "6 PALUAH G1 210_PALUAHg.fastq PALUAH_G1.fastq"
  802. ]
  803. },
  804. "execution_count": 27,
  805. "metadata": {},
  806. "output_type": "execute_result"
  807. }
  808. ],
  809. "source": [
  810. "head(dl)"
  811. ]
  812. },
  813. {
  814. "cell_type": "code",
  815. "execution_count": 28,
  816. "metadata": {
  817. "collapsed": true
  818. },
  819. "outputs": [],
  820. "source": [
  821. "cmdString=paste(\"mv\",dl$V3,dl$V4)"
  822. ]
  823. },
  824. {
  825. "cell_type": "code",
  826. "execution_count": 29,
  827. "metadata": {
  828. "collapsed": false
  829. },
  830. "outputs": [
  831. {
  832. "data": {
  833. "text/html": [
  834. "<ol class=list-inline>\n",
  835. "\t<li>'mv 001_02LRT140414PALTICs_CGATGT.fastq PALTIC_S.fastq'</li>\n",
  836. "\t<li>'mv 209_PALTICg.fastq PALTIC_G1.fastq'</li>\n",
  837. "\t<li>'mv 003_05LRT140414PALTWSs_ACAGTG.fastq PALTWS_S.fastq'</li>\n",
  838. "\t<li>'mv 004_06LRT140414PALTWSg1_GCCAAT.fastq PALTWS_G1.fastq'</li>\n",
  839. "\t<li>'mv 211_PALUAHs.fastq PALUAH_S.fastq'</li>\n",
  840. "\t<li>'mv 210_PALUAHg.fastq PALUAH_G1.fastq'</li>\n",
  841. "</ol>\n"
  842. ],
  843. "text/latex": [
  844. "\\begin{enumerate*}\n",
  845. "\\item 'mv 001_02LRT140414PALTICs_CGATGT.fastq PALTIC_S.fastq'\n",
  846. "\\item 'mv 209_PALTICg.fastq PALTIC_G1.fastq'\n",
  847. "\\item 'mv 003_05LRT140414PALTWSs_ACAGTG.fastq PALTWS_S.fastq'\n",
  848. "\\item 'mv 004_06LRT140414PALTWSg1_GCCAAT.fastq PALTWS_G1.fastq'\n",
  849. "\\item 'mv 211_PALUAHs.fastq PALUAH_S.fastq'\n",
  850. "\\item 'mv 210_PALUAHg.fastq PALUAH_G1.fastq'\n",
  851. "\\end{enumerate*}\n"
  852. ],
  853. "text/markdown": [
  854. "1. 'mv 001_02LRT140414PALTICs_CGATGT.fastq PALTIC_S.fastq'\n",
  855. "2. 'mv 209_PALTICg.fastq PALTIC_G1.fastq'\n",
  856. "3. 'mv 003_05LRT140414PALTWSs_ACAGTG.fastq PALTWS_S.fastq'\n",
  857. "4. 'mv 004_06LRT140414PALTWSg1_GCCAAT.fastq PALTWS_G1.fastq'\n",
  858. "5. 'mv 211_PALUAHs.fastq PALUAH_S.fastq'\n",
  859. "6. 'mv 210_PALUAHg.fastq PALUAH_G1.fastq'\n",
  860. "\n",
  861. "\n"
  862. ],
  863. "text/plain": [
  864. "[1] \"mv 001_02LRT140414PALTICs_CGATGT.fastq PALTIC_S.fastq\" \n",
  865. "[2] \"mv 209_PALTICg.fastq PALTIC_G1.fastq\" \n",
  866. "[3] \"mv 003_05LRT140414PALTWSs_ACAGTG.fastq PALTWS_S.fastq\" \n",
  867. "[4] \"mv 004_06LRT140414PALTWSg1_GCCAAT.fastq PALTWS_G1.fastq\"\n",
  868. "[5] \"mv 211_PALUAHs.fastq PALUAH_S.fastq\" \n",
  869. "[6] \"mv 210_PALUAHg.fastq PALUAH_G1.fastq\" "
  870. ]
  871. },
  872. "execution_count": 29,
  873. "metadata": {},
  874. "output_type": "execute_result"
  875. }
  876. ],
  877. "source": [
  878. "head(cmdString)"
  879. ]
  880. },
  881. {
  882. "cell_type": "code",
  883. "execution_count": 30,
  884. "metadata": {
  885. "collapsed": false
  886. },
  887. "outputs": [
  888. {
  889. "name": "stdout",
  890. "output_type": "stream",
  891. "text": [
  892. "[1] \"mv 001_02LRT140414PALTICs_CGATGT.fastq PALTIC_S.fastq\"\n",
  893. "[1] \"mv 209_PALTICg.fastq PALTIC_G1.fastq\"\n",
  894. "[1] \"mv 003_05LRT140414PALTWSs_ACAGTG.fastq PALTWS_S.fastq\"\n",
  895. "[1] \"mv 004_06LRT140414PALTWSg1_GCCAAT.fastq PALTWS_G1.fastq\"\n",
  896. "[1] \"mv 211_PALUAHs.fastq PALUAH_S.fastq\"\n",
  897. "[1] \"mv 210_PALUAHg.fastq PALUAH_G1.fastq\"\n",
  898. "[1] \"mv 007_13LRT140414PALUCRs_AGTCAA.fastq PALUCR_S.fastq\"\n",
  899. "[1] \"mv 152_14PALUCRg140422.fastq PALUCR_G1.fastq\"\n",
  900. "[1] \"mv 213_PALXCXs.fastq PALXCX_S.fastq\"\n",
  901. "[1] \"mv 212_PALXCXg.fastq PALXCX_G1.fastq\"\n",
  902. "[1] \"mv 011_18LRT140414PAMBWSs_GTCCGC.fastq PAMBWS_S.fastq\"\n",
  903. "[1] \"mv 012_19LRT140414PAMBWSg1_GTGAAA.fastq PAMBWS_G1.fastq\"\n",
  904. "[1] \"mv 195_PALFWKs.fastq PALFWK_S.fastq\"\n",
  905. "[1] \"mv 194_PALFWKg.fastq PALFWK_G1.fastq\"\n",
  906. "[1] \"mv 198_PALIBNs.fastq PALIBN_S.fastq\"\n",
  907. "[1] \"mv 197_PALIBNg.fastq PALIBN_G1.fastq\"\n",
  908. "[1] \"mv 200_PALIYCs.fastq PALIYC_S.fastq\"\n",
  909. "[1] \"mv 199_PALIYCg.fastq PALIYC_G1.fastq\"\n",
  910. "[1] \"mv 228_PAMFDXs.fastq PAMFDX_S.fastq\"\n",
  911. "[1] \"mv 216_PAMFDXg.fastq PAMFDX_G1.fastq\"\n",
  912. "[1] \"mv 021_05PAMHUKs120812_ACAGTG.fastq PAMHUK_S.fastq\"\n",
  913. "[1] \"mv 217_PAMHUKg.fastq PAMHUK_G1.fastq\"\n",
  914. "[1] \"mv 218_PAMVRDs.fastq PAMVRD_S.fastq\"\n",
  915. "[1] \"mv 219_PAMVRDg.fastq PAMVRD_G1.fastq\"\n",
  916. "[1] \"mv 220_PAMYIYs.fastq PAMYIY_S.fastq\"\n",
  917. "[1] \"mv 221_PAMYIYg.fastq PAMYIY_G1.fastq\"\n",
  918. "[1] \"mv 027_15PANAFRs120812_ATGTCA.fastq PANAFR_S.fastq\"\n",
  919. "[1] \"mv 222_PANAFRg.fastq PANAFR_G1.fastq\"\n",
  920. "[1] \"mv 224_PANBULs.fastq PANBUL_S.fastq\"\n",
  921. "[1] \"mv 223_PANBULg.fastq PANBUL_G1.fastq\"\n",
  922. "[1] \"mv 031_02LRT140413_CGATGT.fastq PAMBWY_S.fastq\"\n",
  923. "[1] \"mv 032_04LRT140413_TGACCA.fastq PAMBWY_G1.fastq\"\n",
  924. "[1] \"mv 033_05LRT140413_ACAGTG.fastq PAMDRM_S.fastq\"\n",
  925. "[1] \"mv 034_06LRT140413_GCCAAT.fastq PAMDRM_G1.fastq\"\n",
  926. "[1] \"mv 215_PAMERRs.fastq PAMERR_S.fastq\"\n",
  927. "[1] \"mv 214_PAMERRg.fastq PAMERR_G1.fastq\"\n",
  928. "[1] \"mv 202_PALNTBs.fastq PALNTB_S.fastq\"\n",
  929. "[1] \"mv 201_PALNTBg.fastq PALNTB_G1.fastq\"\n",
  930. "[1] \"mv 039_15PALPHRs140515_ATGTCA.fastq PALPHR_S.fastq\"\n",
  931. "[1] \"mv 203_PALPHRg.fastq PALPHR_G1.fastq\"\n",
  932. "[1] \"mv 205_PALSERs.fastq PALSER_S.fastq\"\n",
  933. "[1] \"mv 204_PALSERg.fastq PALSER_G1.fastq\"\n",
  934. "[1] \"mv 045_05PANFDPs141001_ACAGTG.fastq PANFDP_S.fastq\"\n",
  935. "[1] \"mv 046_06PANFDPg1401002_GCCAAT.fastq PANFDP_G1.fastq\"\n",
  936. "[1] \"mv 047_07PANILLs141001_CAGATC.fastq PANILL_S.fastq\"\n",
  937. "[1] \"mv 048_12PANILLg141001_CTTGTA.fastq PANILL_G1.fastq\"\n",
  938. "[1] \"mv 226_PANLXUs.fastq PANLXU_S.fastq\"\n",
  939. "[1] \"mv 225_PANLXUg.fastq PANLXU_G1.fastq\"\n",
  940. "[1] \"mv 208_PALSSJs.fastq PALSSJ_S.fastq\"\n",
  941. "[1] \"mv 207_PALSSJg.fastq PALSSJ_G1.fastq\"\n",
  942. "[1] \"mv 075_PAIXGPs.fastq PAIXGP_S.fastq\"\n",
  943. "[1] \"mv 178_PAIXGPg.fastq PAIXGP_G1.fastq\"\n",
  944. "[1] \"mv 180_PAIXPHs.fastq PAIXPH_S.fastq\"\n",
  945. "[1] \"mv 179_PAIXPHg.fastq PAIXPH_G1.fastq\"\n",
  946. "[1] \"mv 182_PAKHSVs.fastq PAKHSV_S.fastq\"\n",
  947. "[1] \"mv 181_PAKHSVg.fastq PAKHSV_G1.fastq\"\n",
  948. "[1] \"mv 059_10PAKKMWs141002_TAGCTT.fastq PAKKMW_S.fastq\"\n",
  949. "[1] \"mv 060_11PAKKMWg141001_GGCTAC.fastq PAKKMW_G1.fastq\"\n",
  950. "[1] \"mv 184_PAKUMZs.fastq PAKUMZ_S.fastq\"\n",
  951. "[1] \"mv 183_PAKUMZg.fastq PAKUMZ_G1.fastq\"\n",
  952. "[1] \"mv 063_22PALAURs141002_CGTACG.fastq PALAUR_S.fastq\"\n",
  953. "[1] \"mv 185_PALAURg.fastq PALAUR_G1.fastq\"\n",
  954. "[1] \"mv 187_PALBFBs.fastq PALBFB_S.fastq\"\n",
  955. "[1] \"mv 186_PALBFBg.fastq PALBFB_G1.fastq\"\n",
  956. "[1] \"mv 189_PALBLMs.fastq PALBLM_S.fastq\"\n",
  957. "[1] \"mv 188_PALBLMg.fastq PALBLM_G1.fastq\"\n",
  958. "[1] \"mv 122_05PAKGHNs150318_ACAGTG.fastq PAKGHN_S.fastq\"\n",
  959. "[1] \"mv 123_06PAKGHNg150318_GCCAAT.fastq PAKGHN_G1.fastq\"\n",
  960. "[1] \"mv 140_02PAKFNIs150407_CGATGT.fastq PAKFNI_S.fastq\"\n",
  961. "[1] \"mv 141_04PAKFNIg150407_TGACCA.fastq PAKFNI_G1.fastq\"\n",
  962. "[1] \"mv 128_15PAKGUAs150318_ATGTCA.fastq PAKGUA_S.fastq\"\n",
  963. "[1] \"mv 129_16PAKGUAg150318_CCGTCC.fastq PAKGUA_G1.fastq\"\n",
  964. "[1] \"mv 130_18PAKHJJs150318_GTCCGC.fastq PAKHJJ_S.fastq\"\n",
  965. "[1] \"mv 131_19PAKHJJg150318_GTGAAA.fastq PAKHJJ_G1.fastq\"\n",
  966. "[1] \"mv 126_13PAKHSBs150318_AGTCAA.fastq PAKHSB_S.fastq\"\n",
  967. "[1] \"mv 127_14PAKHSBg150318_AGTTCC.fastq PAKHSB_G1.fastq\"\n",
  968. "[1] \"mv 124_07PAKHSHs150318_CAGATC.fastq PAKHSH_S.fastq\"\n",
  969. "[1] \"mv 125_12PAKHSHg150318_CTTGTA.fastq PAKHSH_G1.fastq\"\n",
  970. "[1] \"mv 142_05PAKHULs150407_ACAGTG.fastq PAKHUL_S.fastq\"\n",
  971. "[1] \"mv 143_06PAKHULg150407_GCCAAT.fastq PAKHUL_G1.fastq\"\n",
  972. "[1] \"mv 144_07PALFGPs150407_CAGATC.fastq PALFGP_S.fastq\"\n",
  973. "[1] \"mv 145_12PALFGPg150407_CTTGTA.fastq PALFGP_G1.fastq\"\n",
  974. "[1] \"mv 148_15PALJVLs150407_ATGTCA.fastq PALJVL_S.fastq\"\n",
  975. "[1] \"mv 149_16PALJVLg150407_CCGTCC.fastq PALJVL_G1.fastq\"\n",
  976. "[1] \"mv 132_01PALKYTs150318_ATCACG.fastq PALKYT_S.fastq\"\n",
  977. "[1] \"mv 133_03PALKYTg150318_TTAGGC.fastq PALKYT_G1.fastq\"\n",
  978. "[1] \"mv 134_08PALMSXs150318_ACTTGA.fastq PALMSX_S.fastq\"\n",
  979. "[1] \"mv 135_09PALMSXg150318_GATCAG.fastq PALMSX_G1.fastq\"\n",
  980. "[1] \"mv 150_18PALNLDs150407_GTCCGC.fastq PALNLD_S.fastq\"\n",
  981. "[1] \"mv 151_19PALNLDg150407_GTGAAA.fastq PALNLD_G1.fastq\"\n",
  982. "[1] \"mv 136_10PALNUAs150318_TAGCTT.fastq PALNUA_S.fastq\"\n",
  983. "[1] \"mv 137_11PALNUAg150318_GGCTAC.fastq PALNUA_G1.fastq\"\n",
  984. "[1] \"mv 138_20PALPEMs150318_GTGGCC.fastq PALPEM_S.fastq\"\n",
  985. "[1] \"mv 139_21PALPEMg150318_GTTTCG.fastq PALPEM_G1.fastq\"\n",
  986. "[1] \"mv 120_02PAIXFKs150318_CGATGT.fastq PAIXFK_S.fastq\"\n",
  987. "[1] \"mv 177_PAIXFKg.fastq PAIXFK_G1.fastq\"\n",
  988. "[1] \"mv 191_PALDNVs.fastq PALDNV_S.fastq\"\n",
  989. "[1] \"mv 190_PALDNAg.fastq PALDNV_G1.fastq\"\n",
  990. "[1] \"mv 206_PALSICs.fastq PALSJC_S.fastq\"\n",
  991. "[1] \"mv 227_PALSJCg.fastq PALSJC_G1.fastq\"\n",
  992. "[1] \"mv 193_PALEZSs.fastq PALEZS_S.fastq\"\n",
  993. "[1] \"mv 192_PALEZSg.fastq PALEZS_G1.fastq\"\n",
  994. "[1] \"mv 196_PALHPAs.fastq PALHPA_S.fastq\"\n",
  995. "[1] \"mv 147_14PALHPAg150407_AGTTCC.fastq PALHPA_G1.fastq\"\n"
  996. ]
  997. }
  998. ],
  999. "source": [
  1000. "res <- rage.run(cmdString)"
  1001. ]
  1002. },
  1003. {
  1004. "cell_type": "code",
  1005. "execution_count": 31,
  1006. "metadata": {
  1007. "collapsed": true
  1008. },
  1009. "outputs": [],
  1010. "source": [
  1011. "s=files(\"*_S.fastq\")"
  1012. ]
  1013. },
  1014. {
  1015. "cell_type": "code",
  1016. "execution_count": 32,
  1017. "metadata": {
  1018. "collapsed": true
  1019. },
  1020. "outputs": [],
  1021. "source": [
  1022. "g=files(\"*_G1.fastq\")"
  1023. ]
  1024. },
  1025. {
  1026. "cell_type": "code",
  1027. "execution_count": 33,
  1028. "metadata": {
  1029. "collapsed": false
  1030. },
  1031. "outputs": [
  1032. {
  1033. "data": {
  1034. "text/html": [
  1035. "<table>\n",
  1036. "<thead><tr><th></th><th scope=col>s</th><th scope=col>g</th></tr></thead>\n",
  1037. "<tbody>\n",
  1038. "\t<tr><th scope=row>1</th><td>PAIXFK_S.fastq</td><td>PAIXFK_G1.fastq</td></tr>\n",
  1039. "\t<tr><th scope=row>2</th><td>PAIXGP_S.fastq</td><td>PAIXGP_G1.fastq</td></tr>\n",
  1040. "\t<tr><th scope=row>3</th><td>PAIXPH_S.fastq</td><td>PAIXPH_G1.fastq</td></tr>\n",
  1041. "\t<tr><th scope=row>4</th><td>PAKFNI_S.fastq</td><td>PAKFNI_G1.fastq</td></tr>\n",
  1042. "\t<tr><th scope=row>5</th><td>PAKGHN_S.fastq</td><td>PAKGHN_G1.fastq</td></tr>\n",
  1043. "\t<tr><th scope=row>6</th><td>PAKGUA_S.fastq</td><td>PAKGUA_G1.fastq</td></tr>\n",
  1044. "\t<tr><th scope=row>7</th><td>PAKHJJ_S.fastq</td><td>PAKHJJ_G1.fastq</td></tr>\n",
  1045. "\t<tr><th scope=row>8</th><td>PAKHSB_S.fastq</td><td>PAKHSB_G1.fastq</td></tr>\n",
  1046. "\t<tr><th scope=row>9</th><td>PAKHSH_S.fastq</td><td>PAKHSH_G1.fastq</td></tr>\n",
  1047. "\t<tr><th scope=row>10</th><td>PAKHSV_S.fastq</td><td>PAKHSV_G1.fastq</td></tr>\n",
  1048. "\t<tr><th scope=row>11</th><td>PAKHUL_S.fastq</td><td>PAKHUL_G1.fastq</td></tr>\n",
  1049. "\t<tr><th scope=row>12</th><td>PAKKMW_S.fastq</td><td>PAKKMW_G1.fastq</td></tr>\n",
  1050. "\t<tr><th scope=row>13</th><td>PAKUMZ_S.fastq</td><td>PAKUMZ_G1.fastq</td></tr>\n",
  1051. "\t<tr><th scope=row>14</th><td>PALAUR_S.fastq</td><td>PALAUR_G1.fastq</td></tr>\n",
  1052. "\t<tr><th scope=row>15</th><td>PALBFB_S.fastq</td><td>PALBFB_G1.fastq</td></tr>\n",
  1053. "\t<tr><th scope=row>16</th><td>PALBLM_S.fastq</td><td>PALBLM_G1.fastq</td></tr>\n",
  1054. "\t<tr><th scope=row>17</th><td>PALDNV_S.fastq</td><td>PALDNV_G1.fastq</td></tr>\n",
  1055. "\t<tr><th scope=row>18</th><td>PALEZS_S.fastq</td><td>PALEZS_G1.fastq</td></tr>\n",
  1056. "\t<tr><th scope=row>19</th><td>PALFGP_S.fastq</td><td>PALFGP_G1.fastq</td></tr>\n",
  1057. "\t<tr><th scope=row>20</th><td>PALFWK_S.fastq</td><td>PALFWK_G1.fastq</td></tr>\n",
  1058. "\t<tr><th scope=row>21</th><td>PALHPA_S.fastq</td><td>PALHPA_G1.fastq</td></tr>\n",
  1059. "\t<tr><th scope=row>22</th><td>PALIBN_S.fastq</td><td>PALIBN_G1.fastq</td></tr>\n",
  1060. "\t<tr><th scope=row>23</th><td>PALIYC_S.fastq</td><td>PALIYC_G1.fastq</td></tr>\n",
  1061. "\t<tr><th scope=row>24</th><td>PALJVL_S.fastq</td><td>PALJVL_G1.fastq</td></tr>\n",
  1062. "\t<tr><th scope=row>25</th><td>PALKYT_S.fastq</td><td>PALKYT_G1.fastq</td></tr>\n",
  1063. "\t<tr><th scope=row>26</th><td>PALMSX_S.fastq</td><td>PALMSX_G1.fastq</td></tr>\n",
  1064. "\t<tr><th scope=row>27</th><td>PALNLD_S.fastq</td><td>PALNLD_G1.fastq</td></tr>\n",
  1065. "\t<tr><th scope=row>28</th><td>PALNTB_S.fastq</td><td>PALNTB_G1.fastq</td></tr>\n",
  1066. "\t<tr><th scope=row>29</th><td>PALNUA_S.fastq</td><td>PALNUA_G1.fastq</td></tr>\n",
  1067. "\t<tr><th scope=row>30</th><td>PALPEM_S.fastq</td><td>PALPEM_G1.fastq</td></tr>\n",
  1068. "\t<tr><th scope=row>31</th><td>PALPHR_S.fastq</td><td>PALPHR_G1.fastq</td></tr>\n",
  1069. "\t<tr><th scope=row>32</th><td>PALSER_S.fastq</td><td>PALSER_G1.fastq</td></tr>\n",
  1070. "\t<tr><th scope=row>33</th><td>PALSJC_S.fastq</td><td>PALSJC_G1.fastq</td></tr>\n",
  1071. "\t<tr><th scope=row>34</th><td>PALSSJ_S.fastq</td><td>PALSSJ_G1.fastq</td></tr>\n",
  1072. "\t<tr><th scope=row>35</th><td>PALTIC_S.fastq</td><td>PALTIC_G1.fastq</td></tr>\n",
  1073. "\t<tr><th scope=row>36</th><td>PALTWS_S.fastq</td><td>PALTWS_G1.fastq</td></tr>\n",
  1074. "\t<tr><th scope=row>37</th><td>PALUAH_S.fastq</td><td>PALUAH_G1.fastq</td></tr>\n",
  1075. "\t<tr><th scope=row>38</th><td>PALUCR_S.fastq</td><td>PALUCR_G1.fastq</td></tr>\n",
  1076. "\t<tr><th scope=row>39</th><td>PALXCX_S.fastq</td><td>PALXCX_G1.fastq</td></tr>\n",
  1077. "\t<tr><th scope=row>40</th><td>PAMBWS_S.fastq</td><td>PAMBWS_G1.fastq</td></tr>\n",
  1078. "\t<tr><th scope=row>41</th><td>PAMBWY_S.fastq</td><td>PAMBWY_G1.fastq</td></tr>\n",
  1079. "\t<tr><th scope=row>42</th><td>PAMDRM_S.fastq</td><td>PAMDRM_G1.fastq</td></tr>\n",
  1080. "\t<tr><th scope=row>43</th><td>PAMERR_S.fastq</td><td>PAMERR_G1.fastq</td></tr>\n",
  1081. "\t<tr><th scope=row>44</th><td>PAMFDX_S.fastq</td><td>PAMFDX_G1.fastq</td></tr>\n",
  1082. "\t<tr><th scope=row>45</th><td>PAMHUK_S.fastq</td><td>PAMHUK_G1.fastq</td></tr>\n",
  1083. "\t<tr><th scope=row>46</th><td>PAMVRD_S.fastq</td><td>PAMVRD_G1.fastq</td></tr>\n",
  1084. "\t<tr><th scope=row>47</th><td>PAMYIY_S.fastq</td><td>PAMYIY_G1.fastq</td></tr>\n",
  1085. "\t<tr><th scope=row>48</th><td>PANAFR_S.fastq</td><td>PANAFR_G1.fastq</td></tr>\n",
  1086. "\t<tr><th scope=row>49</th><td>PANBUL_S.fastq</td><td>PANBUL_G1.fastq</td></tr>\n",
  1087. "\t<tr><th scope=row>50</th><td>PANFDP_S.fastq</td><td>PANFDP_G1.fastq</td></tr>\n",
  1088. "\t<tr><th scope=row>51</th><td>PANILL_S.fastq</td><td>PANILL_G1.fastq</td></tr>\n",
  1089. "\t<tr><th scope=row>52</th><td>PANLXU_S.fastq</td><td>PANLXU_G1.fastq</td></tr>\n",
  1090. "</tbody>\n",
  1091. "</table>\n"
  1092. ],
  1093. "text/latex": [
  1094. "\\begin{tabular}{r|ll}\n",
  1095. " & s & g\\\\\n",
  1096. "\\hline\n",
  1097. "\t1 & PAIXFK_S.fastq & PAIXFK_G1.fastq\\\\\n",
  1098. "\t2 & PAIXGP_S.fastq & PAIXGP_G1.fastq\\\\\n",
  1099. "\t3 & PAIXPH_S.fastq & PAIXPH_G1.fastq\\\\\n",
  1100. "\t4 & PAKFNI_S.fastq & PAKFNI_G1.fastq\\\\\n",
  1101. "\t5 & PAKGHN_S.fastq & PAKGHN_G1.fastq\\\\\n",
  1102. "\t6 & PAKGUA_S.fastq & PAKGUA_G1.fastq\\\\\n",
  1103. "\t7 & PAKHJJ_S.fastq & PAKHJJ_G1.fastq\\\\\n",
  1104. "\t8 & PAKHSB_S.fastq & PAKHSB_G1.fastq\\\\\n",
  1105. "\t9 & PAKHSH_S.fastq & PAKHSH_G1.fastq\\\\\n",
  1106. "\t10 & PAKHSV_S.fastq & PAKHSV_G1.fastq\\\\\n",
  1107. "\t11 & PAKHUL_S.fastq & PAKHUL_G1.fastq\\\\\n",
  1108. "\t12 & PAKKMW_S.fastq & PAKKMW_G1.fastq\\\\\n",
  1109. "\t13 & PAKUMZ_S.fastq & PAKUMZ_G1.fastq\\\\\n",
  1110. "\t14 & PALAUR_S.fastq & PALAUR_G1.fastq\\\\\n",
  1111. "\t15 & PALBFB_S.fastq & PALBFB_G1.fastq\\\\\n",
  1112. "\t16 & PALBLM_S.fastq & PALBLM_G1.fastq\\\\\n",
  1113. "\t17 & PALDNV_S.fastq & PALDNV_G1.fastq\\\\\n",
  1114. "\t18 & PALEZS_S.fastq & PALEZS_G1.fastq\\\\\n",
  1115. "\t19 & PALFGP_S.fastq & PALFGP_G1.fastq\\\\\n",
  1116. "\t20 & PALFWK_S.fastq & PALFWK_G1.fastq\\\\\n",
  1117. "\t21 & PALHPA_S.fastq & PALHPA_G1.fastq\\\\\n",
  1118. "\t22 & PALIBN_S.fastq & PALIBN_G1.fastq\\\\\n",
  1119. "\t23 & PALIYC_S.fastq & PALIYC_G1.fastq\\\\\n",
  1120. "\t24 & PALJVL_S.fastq & PALJVL_G1.fastq\\\\\n",
  1121. "\t25 & PALKYT_S.fastq & PALKYT_G1.fastq\\\\\n",
  1122. "\t26 & PALMSX_S.fastq & PALMSX_G1.fastq\\\\\n",
  1123. "\t27 & PALNLD_S.fastq & PALNLD_G1.fastq\\\\\n",
  1124. "\t28 & PALNTB_S.fastq & PALNTB_G1.fastq\\\\\n",
  1125. "\t29 & PALNUA_S.fastq & PALNUA_G1.fastq\\\\\n",
  1126. "\t30 & PALPEM_S.fastq & PALPEM_G1.fastq\\\\\n",
  1127. "\t31 & PALPHR_S.fastq & PALPHR_G1.fastq\\\\\n",
  1128. "\t32 & PALSER_S.fastq & PALSER_G1.fastq\\\\\n",
  1129. "\t33 & PALSJC_S.fastq & PALSJC_G1.fastq\\\\\n",
  1130. "\t34 & PALSSJ_S.fastq & PALSSJ_G1.fastq\\\\\n",
  1131. "\t35 & PALTIC_S.fastq & PALTIC_G1.fastq\\\\\n",
  1132. "\t36 & PALTWS_S.fastq & PALTWS_G1.fastq\\\\\n",
  1133. "\t37 & PALUAH_S.fastq & PALUAH_G1.fastq\\\\\n",
  1134. "\t38 & PALUCR_S.fastq & PALUCR_G1.fastq\\\\\n",
  1135. "\t39 & PALXCX_S.fastq & PALXCX_G1.fastq\\\\\n",
  1136. "\t40 & PAMBWS_S.fastq & PAMBWS_G1.fastq\\\\\n",
  1137. "\t41 & PAMBWY_S.fastq & PAMBWY_G1.fastq\\\\\n",
  1138. "\t42 & PAMDRM_S.fastq & PAMDRM_G1.fastq\\\\\n",
  1139. "\t43 & PAMERR_S.fastq & PAMERR_G1.fastq\\\\\n",
  1140. "\t44 & PAMFDX_S.fastq & PAMFDX_G1.fastq\\\\\n",
  1141. "\t45 & PAMHUK_S.fastq & PAMHUK_G1.fastq\\\\\n",
  1142. "\t46 & PAMVRD_S.fastq & PAMVRD_G1.fastq\\\\\n",
  1143. "\t47 & PAMYIY_S.fastq & PAMYIY_G1.fastq\\\\\n",
  1144. "\t48 & PANAFR_S.fastq & PANAFR_G1.fastq\\\\\n",
  1145. "\t49 & PANBUL_S.fastq & PANBUL_G1.fastq\\\\\n",
  1146. "\t50 & PANFDP_S.fastq & PANFDP_G1.fastq\\\\\n",
  1147. "\t51 & PANILL_S.fastq & PANILL_G1.fastq\\\\\n",
  1148. "\t52 & PANLXU_S.fastq & PANLXU_G1.fastq\\\\\n",
  1149. "\\end{tabular}\n"
  1150. ],
  1151. "text/plain": [
  1152. " s g\n",
  1153. "1 PAIXFK_S.fastq PAIXFK_G1.fastq\n",
  1154. "2 PAIXGP_S.fastq PAIXGP_G1.fastq\n",
  1155. "3 PAIXPH_S.fastq PAIXPH_G1.fastq\n",
  1156. "4 PAKFNI_S.fastq PAKFNI_G1.fastq\n",
  1157. "5 PAKGHN_S.fastq PAKGHN_G1.fastq\n",
  1158. "6 PAKGUA_S.fastq PAKGUA_G1.fastq\n",
  1159. "7 PAKHJJ_S.fastq PAKHJJ_G1.fastq\n",
  1160. "8 PAKHSB_S.fastq PAKHSB_G1.fastq\n",
  1161. "9 PAKHSH_S.fastq PAKHSH_G1.fastq\n",
  1162. "10 PAKHSV_S.fastq PAKHSV_G1.fastq\n",
  1163. "11 PAKHUL_S.fastq PAKHUL_G1.fastq\n",
  1164. "12 PAKKMW_S.fastq PAKKMW_G1.fastq\n",
  1165. "13 PAKUMZ_S.fastq PAKUMZ_G1.fastq\n",
  1166. "14 PALAUR_S.fastq PALAUR_G1.fastq\n",
  1167. "15 PALBFB_S.fastq PALBFB_G1.fastq\n",
  1168. "16 PALBLM_S.fastq PALBLM_G1.fastq\n",
  1169. "17 PALDNV_S.fastq PALDNV_G1.fastq\n",
  1170. "18 PALEZS_S.fastq PALEZS_G1.fastq\n",
  1171. "19 PALFGP_S.fastq PALFGP_G1.fastq\n",
  1172. "20 PALFWK_S.fastq PALFWK_G1.fastq\n",
  1173. "21 PALHPA_S.fastq PALHPA_G1.fastq\n",
  1174. "22 PALIBN_S.fastq PALIBN_G1.fastq\n",
  1175. "23 PALIYC_S.fastq PALIYC_G1.fastq\n",
  1176. "24 PALJVL_S.fastq PALJVL_G1.fastq\n",
  1177. "25 PALKYT_S.fastq PALKYT_G1.fastq\n",
  1178. "26 PALMSX_S.fastq PALMSX_G1.fastq\n",
  1179. "27 PALNLD_S.fastq PALNLD_G1.fastq\n",
  1180. "28 PALNTB_S.fastq PALNTB_G1.fastq\n",
  1181. "29 PALNUA_S.fastq PALNUA_G1.fastq\n",
  1182. "30 PALPEM_S.fastq PALPEM_G1.fastq\n",
  1183. "31 PALPHR_S.fastq PALPHR_G1.fastq\n",
  1184. "32 PALSER_S.fastq PALSER_G1.fastq\n",
  1185. "33 PALSJC_S.fastq PALSJC_G1.fastq\n",
  1186. "34 PALSSJ_S.fastq PALSSJ_G1.fastq\n",
  1187. "35 PALTIC_S.fastq PALTIC_G1.fastq\n",
  1188. "36 PALTWS_S.fastq PALTWS_G1.fastq\n",
  1189. "37 PALUAH_S.fastq PALUAH_G1.fastq\n",
  1190. "38 PALUCR_S.fastq PALUCR_G1.fastq\n",
  1191. "39 PALXCX_S.fastq PALXCX_G1.fastq\n",
  1192. "40 PAMBWS_S.fastq PAMBWS_G1.fastq\n",
  1193. "41 PAMBWY_S.fastq PAMBWY_G1.fastq\n",
  1194. "42 PAMDRM_S.fastq PAMDRM_G1.fastq\n",
  1195. "43 PAMERR_S.fastq PAMERR_G1.fastq\n",
  1196. "44 PAMFDX_S.fastq PAMFDX_G1.fastq\n",
  1197. "45 PAMHUK_S.fastq PAMHUK_G1.fastq\n",
  1198. "46 PAMVRD_S.fastq PAMVRD_G1.fastq\n",
  1199. "47 PAMYIY_S.fastq PAMYIY_G1.fastq\n",
  1200. "48 PANAFR_S.fastq PANAFR_G1.fastq\n",
  1201. "49 PANBUL_S.fastq PANBUL_G1.fastq\n",
  1202. "50 PANFDP_S.fastq PANFDP_G1.fastq\n",
  1203. "51 PANILL_S.fastq PANILL_G1.fastq\n",
  1204. "52 PANLXU_S.fastq PANLXU_G1.fastq"
  1205. ]
  1206. },
  1207. "execution_count": 33,
  1208. "metadata": {},
  1209. "output_type": "execute_result"
  1210. }
  1211. ],
  1212. "source": [
  1213. "data.frame(s,g)"
  1214. ]
  1215. },
  1216. {
  1217. "cell_type": "code",
  1218. "execution_count": 34,
  1219. "metadata": {
  1220. "collapsed": false
  1221. },
  1222. "outputs": [
  1223. {
  1224. "data": {
  1225. "text/html": [
  1226. "TRUE"
  1227. ],
  1228. "text/latex": [
  1229. "TRUE"
  1230. ],
  1231. "text/markdown": [
  1232. "TRUE"
  1233. ],
  1234. "text/plain": [
  1235. "[1] TRUE"
  1236. ]
  1237. },
  1238. "execution_count": 34,
  1239. "metadata": {},
  1240. "output_type": "execute_result"
  1241. }
  1242. ],
  1243. "source": [
  1244. "identical(remove.suffix(s,\"_\"),remove.suffix(g,\"_\"))"
  1245. ]
  1246. },
  1247. {
  1248. "cell_type": "code",
  1249. "execution_count": 37,
  1250. "metadata": {
  1251. "collapsed": false
  1252. },
  1253. "outputs": [
  1254. {
  1255. "data": {
  1256. "text/html": [
  1257. "<pre class=language-r><code>function (read1files, indexfile, read2files = NULL, cores = \"max\", \n",
  1258. " alignMode = \"end-to-end\", input = \"-q\", all = FALSE, dovetail = FALSE, \n",
  1259. " discordant = FALSE, mixed = FALSE, unaligned = TRUE, maxInsertSize = 500, \n",
  1260. " minInsertSize = 0, appendIndexToName = FALSE, reorder = FALSE) \n",
  1261. "NULL</code></pre>"
  1262. ],
  1263. "text/latex": [
  1264. "\\begin{minted}{r}\n",
  1265. "function (read1files, indexfile, read2files = NULL, cores = \"max\", \n",
  1266. " alignMode = \"end-to-end\", input = \"-q\", all = FALSE, dovetail = FALSE, \n",
  1267. " discordant = FALSE, mixed = FALSE, unaligned = TRUE, maxInsertSize = 500, \n",
  1268. " minInsertSize = 0, appendIndexToName = FALSE, reorder = FALSE) \n",
  1269. "NULL\n",
  1270. "\\end{minted}"
  1271. ],
  1272. "text/markdown": [
  1273. "```r\n",
  1274. "function (read1files, indexfile, read2files = NULL, cores = \"max\", \n",
  1275. " alignMode = \"end-to-end\", input = \"-q\", all = FALSE, dovetail = FALSE, \n",
  1276. " discordant = FALSE, mixed = FALSE, unaligned = TRUE, maxInsertSize = 500, \n",
  1277. " minInsertSize = 0, appendIndexToName = FALSE, reorder = FALSE) \n",
  1278. "NULL\n",
  1279. "```"
  1280. ],
  1281. "text/plain": [
  1282. "function (read1files, indexfile, read2files = NULL, cores = \"max\", \n",
  1283. " alignMode = \"end-to-end\", input = \"-q\", all = FALSE, dovetail = FALSE, \n",
  1284. " discordant = FALSE, mixed = FALSE, unaligned = TRUE, maxInsertSize = 500, \n",
  1285. " minInsertSize = 0, appendIndexToName = FALSE, reorder = FALSE) \n",
  1286. "NULL"
  1287. ]
  1288. },
  1289. "execution_count": 37,
  1290. "metadata": {},
  1291. "output_type": "execute_result"
  1292. }
  1293. ],
  1294. "source": [
  1295. "args(bowtie2)"
  1296. ]
  1297. },
  1298. {
  1299. "cell_type": "code",
  1300. "execution_count": null,
  1301. "metadata": {
  1302. "collapsed": true
  1303. },
  1304. "outputs": [],
  1305. "source": [
  1306. "sams=bowtie2(c(s,g),\"~/hg38/bowtie2index/genome\",cores=11)"
  1307. ]
  1308. },
  1309. {
  1310. "cell_type": "code",
  1311. "execution_count": null,
  1312. "metadata": {
  1313. "collapsed": true
  1314. },
  1315. "outputs": [],
  1316. "source": []
  1317. }
  1318. ],
  1319. "metadata": {
  1320. "kernelspec": {
  1321. "display_name": "R",
  1322. "language": "R",
  1323. "name": "ir"
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