+"""
+Create simulated solexa/illumina runfolders for testing
+"""
+
+import os
+
+
+def make_ipar_dir(data_dir):
+ """
+ Construct an artificial ipar parameter file and directory
+ """
+ params = """<?xml version="1.0"?>
+<ImageAnalysis>
+ <Run Name="IPAR_1.01">
+ <Software Name="IPAR" Version="2.01.192.0" />
+ <Cycles First="1" Last="37" Number="37" />
+ <RunParameters>
+ <ImagingReads Index="1">
+ <FirstCycle>1</FirstCycle>
+ <LastCycle>37</LastCycle>
+ <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
+ </ImagingReads>
+ <Reads Index="1">
+ <FirstCycle>1</FirstCycle>
+ <LastCycle>37</LastCycle>
+ <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
+ </Reads>
+ <Compression>gzip</Compression>
+ <CompressionSuffix>.p.gz</CompressionSuffix>
+ <Instrument>HWI-EAS229</Instrument>
+ <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
+ </RunParameters>
+ <ImageParameters>
+ <AutoOffsetFlag>1</AutoOffsetFlag>
+ <Fwhm>2.7</Fwhm>
+ <RemappingDistance>1.5</RemappingDistance>
+ <Threshold>4</Threshold>
+ </ImageParameters>
+ <TileSelection>
+ <Lane Index="1">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="2">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="3">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="4">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="5">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="6">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="7">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ <Lane Index="8">
+ <Sample>s</Sample>
+ <TileRange Max="100" Min="1" />
+ </Lane>
+ </TileSelection>
+ </Run>
+</ImageAnalysis>
+"""
+ f = open(os.path.join(data_dir, '.params'),'w')
+ f.write(params)
+ f.close()
+ ipar_dir = os.path.join(data_dir, 'IPAR_1.01')
+ if not os.path.exists(ipar_dir):
+ os.mkdir(ipar_dir)
+ return ipar_dir
+
+def make_flowcell_id(runfolder_dir, flowcell_id=None):
+ if flowcell_id is None:
+ flowcell_id = '207BTAAXY'
+
+ config = """<?xml version="1.0"?>
+<FlowcellId>
+ <Text>%s</Text>
+</FlowcellId>""" % (flowcell_id,)
+ config_dir = os.path.join(runfolder_dir, 'Config')
+
+ if not os.path.exists(config_dir):
+ os.mkdir(config_dir)
+ pathname = os.path.join(config_dir, 'FlowcellId.xml')
+ f = open(pathname,'w')
+ f.write(config)
+ f.close()
+
+def make_matrix(matrix_dir):
+ contents = """# Auto-generated frequency response matrix
+> A
+> C
+> G
+> T
+0.77 0.15 -0.04 -0.04
+0.76 1.02 -0.05 -0.06
+-0.10 -0.10 1.17 -0.03
+-0.13 -0.12 0.80 1.27
+"""
+ s_matrix = os.path.join(matrix_dir, 's_matrix.txt')
+ f = open(s_matrix, 'w')
+ f.write(contents)
+ f.close()
+
+def make_phasing_params(bustard_dir):
+ for lane in range(1,9):
+ pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
+ f = open(pathname, 'w')
+ f.write("""<Parameters>
+ <Phasing>0.009900</Phasing>
+ <Prephasing>0.003500</Prephasing>
+</Parameters>
+""")
+ f.close()
+
+def make_gerald_config(gerald_dir):
+ config_xml = """<RunParameters>
+<ChipWideRunParameters>
+ <ANALYSIS>default</ANALYSIS>
+ <BAD_LANES></BAD_LANES>
+ <BAD_TILES></BAD_TILES>
+ <CONTAM_DIR></CONTAM_DIR>
+ <CONTAM_FILE></CONTAM_FILE>
+ <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
+ <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
+ <ELAND_REPEAT></ELAND_REPEAT>
+ <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
+ <EMAIL_LIST>diane</EMAIL_LIST>
+ <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
+ <EXPT_DIR>/home/diane/gec/080416_HWI-EAS229_0024_207BTAAXX/Data/C1-33_Firecrest1.8.28_19-04-2008_diane/Bustard1.8.28_19-04-2008_diane</EXPT_DIR>
+ <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
+ <FORCE>1</FORCE>
+ <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
+ <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
+ <HAMSTER_FLAG>genome</HAMSTER_FLAG>
+ <OUT_DIR>/home/diane/gec/080416_HWI-EAS229_0024_207BTAAXX/Data/C1-33_Firecrest1.8.28_19-04-2008_diane/Bustard1.8.28_19-04-2008_diane/GERALD_19-04-2008_diane</OUT_DIR>
+ <POST_RUN_COMMAND></POST_RUN_COMMAND>
+ <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
+ <PURE_BASES>12</PURE_BASES>
+ <QF_PARAMS>'((CHASTITY>=0.6))'</QF_PARAMS>
+ <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
+ <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
+ <READ_LENGTH>32</READ_LENGTH>
+ <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
+ <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
+ <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
+ <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
+ <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
+ <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
+ <TILE_ROOT>s</TILE_ROOT>
+ <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
+ <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
+ <USE_BASES>all</USE_BASES>
+ <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
+</ChipWideRunParameters>
+<LaneSpecificRunParameters>
+ <ANALYSIS>
+ <s_1>eland</s_1>
+ <s_2>eland</s_2>
+ <s_3>eland</s_3>
+ <s_4>eland</s_4>
+ <s_5>eland</s_5>
+ <s_6>eland</s_6>
+ <s_7>eland</s_7>
+ <s_8>eland</s_8>
+ </ANALYSIS>
+ <ELAND_GENOME>
+ <s_1>/g/dm3</s_1>
+ <s_2>/g/equcab1</s_2>
+ <s_3>/g/equcab1</s_3>
+ <s_4>/g/canfam2</s_4>
+ <s_5>/g/hg18</s_5>
+ <s_6>/g/hg18</s_6>
+ <s_7>/g/hg18</s_7>
+ <s_8>/g/hg18</s_8>
+ </ELAND_GENOME>
+ <READ_LENGTH>
+ <s_1>32</s_1>
+ <s_2>32</s_2>
+ <s_3>32</s_3>
+ <s_4>32</s_4>
+ <s_5>32</s_5>
+ <s_6>32</s_6>
+ <s_7>32</s_7>
+ <s_8>32</s_8>
+ </READ_LENGTH>
+ <USE_BASES>
+ <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
+ <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
+ <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
+ <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
+ <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
+ <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
+ <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
+ <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
+ </USE_BASES>
+</LaneSpecificRunParameters>
+</RunParameters>
+"""
+ pathname = os.path.join(gerald_dir, 'config.xml')
+ f = open(pathname,'w')
+ f.write(config_xml)
+ f.close()
+
+def make_summary100_htm(gerald_dir):
+ summary_htm="""<!--RUN_TIME Wed Jul 2 06:47:44 2008 -->
+<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
+<html>
+<body>
+
+<a name="Top"><h2><title>080627_HWI-EAS229_0036_3055HAXX Summary</title></h2></a>
+<h1>Summary Information For Experiment 080627_HWI-EAS229_0036_3055HAXX on Machine HWI-EAS229</h1>
+<h2><br></br>Chip Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr><td>Machine</td><td>HWI-EAS229</td></tr>
+<tr><td>Run Folder</td><td>080627_HWI-EAS229_0036_3055HAXX</td></tr>
+<tr><td>Chip ID</td><td>unknown</td></tr>
+</table>
+<h2><br></br>Chip Results Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+<td>Clusters</td>
+<td>Clusters (PF)</td>
+<td>Yield (kbases)</td>
+</tr>
+<tr><td>80933224</td>
+<td>43577803</td>
+<td>1133022</td>
+</tr>
+</table>
+<h2><br></br>Lane Parameter Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane</td>
+<td>Sample ID</td>
+<td>Sample Target</td>
+<td>Sample Type</td>
+<td>Length</td>
+<td>Filter</td>
+<td>Num Tiles</td>
+<td>Tiles</td>
+</tr>
+<tr>
+<td>1</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane1">Lane 1</a></td>
+</tr>
+<tr>
+<td>2</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane2">Lane 2</a></td>
+</tr>
+<tr>
+<td>3</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane3">Lane 3</a></td>
+</tr>
+<tr>
+<td>4</td>
+<td>unknown</td>
+<td>elegans170</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane4">Lane 4</a></td>
+</tr>
+<tr>
+<td>5</td>
+<td>unknown</td>
+<td>elegans170</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane5">Lane 5</a></td>
+</tr>
+<tr>
+<td>6</td>
+<td>unknown</td>
+<td>elegans170</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane6">Lane 6</a></td>
+</tr>
+<tr>
+<td>7</td>
+<td>unknown</td>
+<td>elegans170</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane7">Lane 7</a></td>
+</tr>
+<tr>
+<td>8</td>
+<td>unknown</td>
+<td>elegans170</td>
+<td>ELAND</td>
+<td>26</td>
+<td>'((CHASTITY>=0.6))'</td>
+<td>100</td>
+<td><a href="#Lane8">Lane 8</a></td>
+</tr>
+</table>
+<h2><br></br>Lane Results Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+<td colspan="2">Lane Info</td>
+<td colspan="8">Tile Mean +/- SD for Lane</td>
+</tr>
+<tr>
+<td>Lane </td>
+<td>Lane Yield (kbases) </td>
+<td>Clusters (raw)</td>
+<td>Clusters (PF) </td>
+<td>1st Cycle Int (PF) </td>
+<td>% intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Alignment Score (PF) </td>
+<td> % Error Rate (PF) </td>
+</tr>
+<tr>
+<td>1</td>
+<td>158046</td>
+<td>96483 +/- 9074</td>
+<td>60787 +/- 4240</td>
+<td>329 +/- 35</td>
+<td>101.88 +/- 6.03</td>
+<td>63.21 +/- 3.29</td>
+<td>70.33 +/- 0.24</td>
+<td>9054.08 +/- 59.16</td>
+<td>0.46 +/- 0.18</td>
+</tr>
+<tr>
+<td>2</td>
+<td>156564</td>
+<td>133738 +/- 7938</td>
+<td>60217 +/- 1926</td>
+<td>444 +/- 39</td>
+<td>92.62 +/- 7.58</td>
+<td>45.20 +/- 3.31</td>
+<td>51.98 +/- 0.74</td>
+<td>6692.04 +/- 92.49</td>
+<td>0.46 +/- 0.09</td>
+</tr>
+<tr>
+<td>3</td>
+<td>185818</td>
+<td>152142 +/- 10002</td>
+<td>71468 +/- 2827</td>
+<td>366 +/- 36</td>
+<td>91.53 +/- 8.66</td>
+<td>47.19 +/- 3.80</td>
+<td>82.24 +/- 0.44</td>
+<td>10598.68 +/- 64.13</td>
+<td>0.41 +/- 0.04</td>
+</tr>
+<tr>
+<td>4</td>
+<td>34953</td>
+<td>15784 +/- 2162</td>
+<td>13443 +/- 1728</td>
+<td>328 +/- 40</td>
+<td>97.53 +/- 9.87</td>
+<td>85.29 +/- 1.91</td>
+<td>80.02 +/- 0.53</td>
+<td>10368.82 +/- 71.08</td>
+<td>0.15 +/- 0.05</td>
+</tr>
+<tr>
+<td>5</td>
+<td>167936</td>
+<td>119735 +/- 8465</td>
+<td>64590 +/- 2529</td>
+<td>417 +/- 37</td>
+<td>88.69 +/- 14.79</td>
+<td>54.10 +/- 2.59</td>
+<td>76.95 +/- 0.32</td>
+<td>9936.47 +/- 65.75</td>
+<td>0.28 +/- 0.02</td>
+</tr>
+<tr>
+<td>6</td>
+<td>173463</td>
+<td>152177 +/- 8146</td>
+<td>66716 +/- 2493</td>
+<td>372 +/- 39</td>
+<td>87.06 +/- 9.86</td>
+<td>43.98 +/- 3.12</td>
+<td>78.80 +/- 0.43</td>
+<td>10162.28 +/- 49.65</td>
+<td>0.38 +/- 0.03</td>
+</tr>
+<tr>
+<td>7</td>
+<td>149287</td>
+<td>84649 +/- 7325</td>
+<td>57418 +/- 3617</td>
+<td>295 +/- 28</td>
+<td>89.40 +/- 8.23</td>
+<td>67.97 +/- 1.82</td>
+<td>33.38 +/- 0.25</td>
+<td>4247.92 +/- 32.37</td>
+<td>1.00 +/- 0.03</td>
+</tr>
+<tr>
+<td>8</td>
+<td>106953</td>
+<td>54622 +/- 4812</td>
+<td>41136 +/- 3309</td>
+<td>284 +/- 37</td>
+<td>90.21 +/- 9.10</td>
+<td>75.39 +/- 2.27</td>
+<td>48.33 +/- 0.29</td>
+<td>6169.21 +/- 169.50</td>
+<td>0.86 +/- 1.22</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>101166</td>
+<td>54472</td>
+<td>354</td>
+<td>92.36</td>
+<td>60.29</td>
+<td>65.25</td>
+<td>8403.69</td>
+<td>0.50</td>
+</tr>
+</table>
+<h2><br></br>Expanded Lane Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr>
+
+<tr><td colspan="2">Lane Info</td>
+<td colspan="2">Phasing Info</td>
+<td colspan="2">Raw Data (tile mean)</td>
+<td colspan="7">Filtered Data (tile mean)</td></tr>
+<td>Lane </td>
+<td>Clusters (tile mean) (raw)</td>
+<td>% Phasing </td>
+<td>% Prephasing </td>
+<td>% Error Rate (raw) </td>
+<td> Equiv Perfect Clusters (raw) </td>
+<td>% retained </td>
+<td>Cycle 2-4 Av Int (PF) </td>
+<td>Cycle 2-10 Av % Loss (PF) </td>
+<td>Cycle 10-20 Av % Loss (PF) </td>
+<td>% Align (PF) </td>
+<td>% Error Rate (PF) </td>
+<td> Equiv Perfect Clusters (PF) </td>
+</tr>
+<tr>
+<td>1</td>
+<td>96483</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>1.00</td>
+<td>49676</td>
+<td>63.21</td>
+<td>317 +/- 32</td>
+<td>0.13 +/- 0.44</td>
+<td>-1.14 +/- 0.34</td>
+<td>70.33</td>
+<td>0.46</td>
+<td>41758</td>
+</tr>
+<tr>
+<td>2</td>
+<td>133738</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>1.22</td>
+<td>40467</td>
+<td>45.20</td>
+<td>415 +/- 33</td>
+<td>0.29 +/- 0.40</td>
+<td>-0.79 +/- 0.35</td>
+<td>51.98</td>
+<td>0.46</td>
+<td>30615</td>
+</tr>
+<tr>
+<td>3</td>
+<td>152142</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>1.30</td>
+<td>78588</td>
+<td>47.19</td>
+<td>344 +/- 26</td>
+<td>0.68 +/- 0.51</td>
+<td>-0.77 +/- 0.42</td>
+<td>82.24</td>
+<td>0.41</td>
+<td>57552</td>
+</tr>
+<tr>
+<td>4</td>
+<td>15784</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>0.29</td>
+<td>11095</td>
+<td>85.29</td>
+<td>306 +/- 34</td>
+<td>0.20 +/- 0.69</td>
+<td>-1.28 +/- 0.66</td>
+<td>80.02</td>
+<td>0.15</td>
+<td>10671</td>
+</tr>
+<tr>
+<td>5</td>
+<td>119735</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>0.85</td>
+<td>60335</td>
+<td>54.10</td>
+<td>380 +/- 32</td>
+<td>0.34 +/- 0.49</td>
+<td>-1.55 +/- 4.69</td>
+<td>76.95</td>
+<td>0.28</td>
+<td>49015</td>
+</tr>
+<tr>
+<td>6</td>
+<td>152177</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>1.21</td>
+<td>70905</td>
+<td>43.98</td>
+<td>333 +/- 27</td>
+<td>0.57 +/- 0.50</td>
+<td>-0.91 +/- 0.39</td>
+<td>78.80</td>
+<td>0.38</td>
+<td>51663</td>
+</tr>
+<tr>
+<td>7</td>
+<td>84649</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>1.38</td>
+<td>21069</td>
+<td>67.97</td>
+<td>272 +/- 20</td>
+<td>1.15 +/- 0.52</td>
+<td>-0.84 +/- 0.58</td>
+<td>33.38</td>
+<td>1.00</td>
+<td>18265</td>
+</tr>
+<tr>
+<td>8</td>
+<td>54622</td>
+<td>0.7700</td>
+<td>0.3100</td>
+<td>1.17</td>
+<td>21335</td>
+<td>75.39</td>
+<td>262 +/- 31</td>
+<td>1.10 +/- 0.59</td>
+<td>-1.01 +/- 0.47</td>
+<td>48.33</td>
+<td>0.86</td>
+<td>19104</td>
+</tr>
+</table>
+<b><br></br>IVC Plots</b>
+<p> <a href='IVC.htm' target="_blank"> IVC.htm
+ </a></p>
+<b><br></br>All Intensity Plots</b>
+<p> <a href='All.htm' target="_blank"> All.htm
+ </a></p>
+<b><br></br>Error graphs: </b>
+<p> <a href='Error.htm' target="_blank"> Error.htm
+ </a></p>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane1"><h2><br></br>Lane 1<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>1</td>
+<td>0001</td>
+<td>114972</td>
+<td>326.48</td>
+<td>94.39</td>
+<td>57.44</td>
+<td>70.2</td>
+<td>9038.6</td>
+<td>0.44</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane2"><h2><br></br>Lane 2<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>2</td>
+<td>0001</td>
+<td>147793</td>
+<td>448.12</td>
+<td>83.68</td>
+<td>38.57</td>
+<td>53.7</td>
+<td>6905.4</td>
+<td>0.54</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane3"><h2><br></br>Lane 3<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>3</td>
+<td>0001</td>
+<td>167904</td>
+<td>374.05</td>
+<td>86.91</td>
+<td>40.36</td>
+<td>81.3</td>
+<td>10465.0</td>
+<td>0.47</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane4"><h2><br></br>Lane 4<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>4</td>
+<td>0001</td>
+<td>20308</td>
+<td>276.85</td>
+<td>92.87</td>
+<td>84.26</td>
+<td>80.4</td>
+<td>10413.8</td>
+<td>0.16</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane5"><h2><br></br>Lane 5<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane6"><h2><br></br>Lane 6<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>6</td>
+<td>0001</td>
+<td>166844</td>
+<td>348.12</td>
+<td>77.59</td>
+<td>38.13</td>
+<td>79.7</td>
+<td>10264.4</td>
+<td>0.44</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane7"><h2><br></br>Lane 7<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>7</td>
+<td>0001</td>
+<td>98913</td>
+<td>269.90</td>
+<td>86.66</td>
+<td>64.55</td>
+<td>33.2</td>
+<td>4217.5</td>
+<td>1.02</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+<a name="Lane8"><h2><br></br>Lane 8<br></br></h2></a>
+<table border="1" cellpadding="5">
+<tr>
+<td>Lane </td>
+<td>Tile </td>
+<td>Clusters (raw)</td>
+<td>Av 1st Cycle Int (PF) </td>
+<td>Av % intensity after 20 cycles (PF) </td>
+<td>% PF Clusters </td>
+<td>% Align (PF) </td>
+<td>Av Alignment Score (PF) </td>
+<td>% Error Rate (PF) </td>
+</tr>
+<tr>
+<td>8</td>
+<td>0001</td>
+<td>64972</td>
+<td>243.60</td>
+<td>89.40</td>
+<td>73.17</td>
+<td>48.3</td>
+<td>6182.8</td>
+<td>0.71</td>
+</tr>
+</table>
+<td><a href="#Top">Back to top</a></td>
+</body>
+</html>
+"""
+ pathname = os.path.join(gerald_dir, 'Summary.htm')
+ f = open(pathname, 'w')
+ f.write(summary_htm)
+ f.close()
+
+def make_eland_results(gerald_dir):
+ eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
+>HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T
+>HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
+>HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
+"""
+ for i in range(1,9):
+ pathname = os.path.join(gerald_dir,
+ 's_%d_eland_result.txt' % (i,))
+ f = open(pathname, 'w')
+ f.write(eland_result)
+ f.close()