import os
import shutil
+TEST_CODE_DIR = os.path.split(__file__)[0]
+TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
+
def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
firecrest_dir = os.path.join(data_dir,
'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
"""
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()
+ ipar1_01_file = os.path.join(TESTDATA_DIR, 'IPAR1.01.params')
+ shutil.copy(ipar1_01_file, os.path.join(data_dir, '.params'))
+
ipar_dir = os.path.join(data_dir, 'IPAR_1.01')
if not os.path.exists(ipar_dir):
os.mkdir(ipar_dir)
f.write(config)
f.close()
-def make_matrix(matrix_dir):
+def make_matrix(matrix_filename):
contents = """# Auto-generated frequency response matrix
> A
> C
-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 = open(matrix_filename, 'w')
f.write(contents)
f.close()
""")
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>
+def make_gerald_config_026(gerald_dir):
+ source = os.path.join(TESTDATA_DIR, 'gerald_config_0.2.6.xml')
+ destination = os.path.join(gerald_dir, 'config.xml')
+ shutil.copy(source, destination)
-<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>
+def make_gerald_config_100(gerald_dir):
+ source = os.path.join(TESTDATA_DIR, 'gerald_config_1.0.xml')
+ destination = os.path.join(gerald_dir, 'config.xml')
+ shutil.copy(source, destination)
-<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_summary_htm_100(gerald_dir):
+ source = os.path.join(TESTDATA_DIR, 'Summary-pipeline100.htm')
+ destination = os.path.join(gerald_dir, 'Summary.htm')
+ shutil.copy(source, destination)
def make_summary_htm_110(gerald_dir):
- summary_htm = """<!--RUN_TIME Tue Oct 28 09:45:50 2008 -->
-<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.10 2008/07/23 15:18:30 mzerara Exp $-->
-<html>
-<body>
-
-<a name="Top"><h2><title>081017_HWI-EAS229_0062_30J55AAXX Summary</title></h2></a>
-<h1>Summary Information For Experiment 081017_HWI-EAS229_0062_30J55AAXX 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>081017_HWI-EAS229_0062_30J55AAXX</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>162491175</td>
-<td>99622159</td>
-<td>3686019</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>Chast. Thresh.</td>
-<td>Num Tiles</td>
-<td>Tiles</td>
-</tr>
-<tr>
-<td>1</td>
-<td>unknown</td>
-<td>mm9</td>
-<td>ELAND</td>
-<td>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>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>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>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>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>0.6</td>
-<td>100</td>
-<td><a href="#Lane3">Lane 3</a></td>
-</tr>
-<tr>
-<td>4</td>
-<td>unknown</td>
-<td>hg18</td>
-<td>ELAND</td>
-<td>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>0.6</td>
-<td>100</td>
-<td><a href="#Lane4">Lane 4</a></td>
-</tr>
-<tr>
-<td>5</td>
-<td>unknown</td>
-<td>hg18</td>
-<td>ELAND</td>
-<td>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>0.6</td>
-<td>100</td>
-<td><a href="#Lane5">Lane 5</a></td>
-</tr>
-<tr>
-<td>6</td>
-<td>unknown</td>
-<td>mm9</td>
-<td>ELAND</td>
-<td>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>0.6</td>
-<td>100</td>
-<td><a href="#Lane6">Lane 6</a></td>
-</tr>
-<tr>
-<td>7</td>
-<td>unknown</td>
-<td>mm9</td>
-<td>ELAND</td>
-<td>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>0.6</td>
-<td>100</td>
-<td><a href="#Lane7">Lane 7</a></td>
-</tr>
-<tr>
-<td>8</td>
-<td>unknown</td>
-<td>mm9</td>
-<td>ELAND</td>
-<td>37</td>
-<td>'((FAILED_CHASTITY<=1))'</td>
-<td>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>435340</td>
-<td>190220 +/- 15118</td>
-<td>117659 +/- 8144</td>
-<td>273 +/- 16</td>
-<td>80.02 +/- 2.52</td>
-<td>62.15 +/- 5.54</td>
-<td>77.18 +/- 0.22</td>
-<td>13447.28 +/- 43.35</td>
-<td>2.78 +/- 0.13</td>
-</tr>
-<tr>
-<td>2</td>
-<td>462364</td>
-<td>190560 +/- 14399</td>
-<td>124963 +/- 5687</td>
-<td>271 +/- 16</td>
-<td>75.73 +/- 2.46</td>
-<td>65.83 +/- 4.12</td>
-<td>70.06 +/- 0.39</td>
-<td>12082.95 +/- 64.81</td>
-<td>3.22 +/- 0.09</td>
-</tr>
-<tr>
-<td>3</td>
-<td>468929</td>
-<td>187597 +/- 12369</td>
-<td>126737 +/- 5549</td>
-<td>274 +/- 16</td>
-<td>72.61 +/- 2.67</td>
-<td>67.69 +/- 2.72</td>
-<td>74.03 +/- 0.22</td>
-<td>12470.18 +/- 50.02</td>
-<td>4.27 +/- 0.08</td>
-</tr>
-<tr>
-<td>4</td>
-<td>491642</td>
-<td>204142 +/- 16877</td>
-<td>132876 +/- 4023</td>
-<td>253 +/- 16</td>
-<td>80.43 +/- 3.10</td>
-<td>65.39 +/- 3.84</td>
-<td>72.95 +/- 0.15</td>
-<td>13273.80 +/- 39.75</td>
-<td>0.78 +/- 0.10</td>
-</tr>
-<tr>
-<td>5</td>
-<td>433033</td>
-<td>247308 +/- 11600</td>
-<td>117036 +/- 4489</td>
-<td>273 +/- 11</td>
-<td>68.60 +/- 2.40</td>
-<td>47.48 +/- 3.63</td>
-<td>66.91 +/- 0.54</td>
-<td>11700.08 +/- 66.33</td>
-<td>2.62 +/- 0.13</td>
-</tr>
-<tr>
-<td>6</td>
-<td>483012</td>
-<td>204298 +/- 15640</td>
-<td>130543 +/- 6972</td>
-<td>254 +/- 11</td>
-<td>81.35 +/- 1.96</td>
-<td>64.14 +/- 4.40</td>
-<td>77.28 +/- 0.11</td>
-<td>14084.01 +/- 23.09</td>
-<td>0.71 +/- 0.03</td>
-</tr>
-<tr>
-<td>7</td>
-<td>474325</td>
-<td>202707 +/- 15404</td>
-<td>128196 +/- 9745</td>
-<td>255 +/- 13</td>
-<td>79.95 +/- 2.08</td>
-<td>63.48 +/- 5.63</td>
-<td>75.78 +/- 0.18</td>
-<td>13758.74 +/- 60.86</td>
-<td>0.88 +/- 0.12</td>
-</tr>
-<tr>
-<td>8</td>
-<td>437372</td>
-<td>198075 +/- 14702</td>
-<td>118208 +/- 14798</td>
-<td>259 +/- 14</td>
-<td>81.80 +/- 2.53</td>
-<td>59.85 +/- 7.67</td>
-<td>74.55 +/- 0.36</td>
-<td>13586.07 +/- 103.97</td>
-<td>0.71 +/- 0.15</td>
-</tr>
-<tr><td colspan="13">Tile mean across chip</td></tr>
-<tr>
-<td>Av.</td>
-<td></td>
-<td>203113</td>
-<td>124527</td>
-<td>264</td>
-<td>77.56</td>
-<td>62.00</td>
-<td>73.59</td>
-<td>13050.39</td>
-<td>2.00</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>190220</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>3.17</td>
-<td>107262</td>
-<td>62.15</td>
-<td>241 +/- 13</td>
-<td>0.56 +/- 0.22</td>
-<td>0.29 +/- 0.14</td>
-<td>77.18</td>
-<td>2.78</td>
-<td>86184</td>
-</tr>
-<tr>
-<td>2</td>
-<td>190560</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>3.53</td>
-<td>98678</td>
-<td>65.83</td>
-<td>238 +/- 14</td>
-<td>0.78 +/- 0.15</td>
-<td>0.53 +/- 0.15</td>
-<td>70.06</td>
-<td>3.22</td>
-<td>83090</td>
-</tr>
-<tr>
-<td>3</td>
-<td>187597</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>4.44</td>
-<td>104008</td>
-<td>67.69</td>
-<td>233 +/- 14</td>
-<td>0.56 +/- 0.17</td>
-<td>0.59 +/- 0.26</td>
-<td>74.03</td>
-<td>4.27</td>
-<td>89278</td>
-</tr>
-<tr>
-<td>4</td>
-<td>204142</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>1.38</td>
-<td>115765</td>
-<td>65.39</td>
-<td>239 +/- 14</td>
-<td>1.28 +/- 0.21</td>
-<td>0.77 +/- 0.21</td>
-<td>72.95</td>
-<td>0.78</td>
-<td>93475</td>
-</tr>
-<tr>
-<td>5</td>
-<td>247308</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>3.40</td>
-<td>103006</td>
-<td>47.48</td>
-<td>242 +/- 10</td>
-<td>1.61 +/- 0.39</td>
-<td>1.21 +/- 0.21</td>
-<td>66.91</td>
-<td>2.62</td>
-<td>73768</td>
-</tr>
-<tr>
-<td>6</td>
-<td>204298</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>1.33</td>
-<td>122233</td>
-<td>64.14</td>
-<td>242 +/- 12</td>
-<td>1.30 +/- 0.11</td>
-<td>0.73 +/- 0.22</td>
-<td>77.28</td>
-<td>0.71</td>
-<td>97646</td>
-</tr>
-<tr>
-<td>7</td>
-<td>202707</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>1.51</td>
-<td>117513</td>
-<td>63.48</td>
-<td>238 +/- 13</td>
-<td>1.27 +/- 0.38</td>
-<td>0.66 +/- 0.22</td>
-<td>75.78</td>
-<td>0.88</td>
-<td>93659</td>
-</tr>
-<tr>
-<td>8</td>
-<td>198075</td>
-<td>0.6800</td>
-<td>0.2800</td>
-<td>1.41</td>
-<td>111115</td>
-<td>59.85</td>
-<td>244 +/- 12</td>
-<td>1.19 +/- 0.16</td>
-<td>0.65 +/- 0.29</td>
-<td>74.55</td>
-<td>0.71</td>
-<td>85327</td>
-</tr>
-</table>
-</body>
-</html>"""
- pathname = os.path.join(gerald_dir, 'Summary.htm')
- f = open(pathname, 'w')
- f.write(summary_htm)
- f.close()
+ source = os.path.join(TESTDATA_DIR, 'Summary-pipeline110.htm')
+ destination = os.path.join(gerald_dir, 'Summary.htm')
+ shutil.copy(source, destination)
def make_summary_paired_htm(gerald_dir):
- summary_htm = """<!--RUN_TIME Thu Nov 13 15:11:29 2008 -->
-<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
-<html>
-<body>
-
-<a name="Top"><h2><title>080920_HWI-EAS229_0057_30GBJAAXX Summary</title></h2></a>
-<h1>Summary Information For Experiment 080920_HWI-EAS229_0057_30GBJAAXX on Machine unknown</h1>
-<h2><br></br>Chip Summary<br></br></h2>
-<table border="1" cellpadding="5">
-<tr><td>Machine</td><td>UNKNOWN</td></tr>
-<tr><td>Run Folder</td><td>080920_HWI-EAS229_0057_30GBJAAXX</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>126151880</td>
-<td>95923456</td>
-<td>3549167</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_PAIR</td>
-<td>37, 37</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>hg18</td>
-<td>ELAND_PAIR</td>
-<td>37, 37</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_PAIR</td>
-<td>37, 37</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>mm9</td>
-<td>ELAND_PAIR</td>
-<td>37, 37</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>mm9</td>
-<td>ELAND_PAIR</td>
-<td>37, 37</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>hg18</td>
-<td>ELAND_PAIR</td>
-<td>37, 37</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>mm9</td>
-<td>ELAND_PAIR</td>
-<td>37, 37</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>mm9</td>
-<td>ELAND_PAIR</td>
-<td>37, 37</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 : Read 1<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>277083</td>
-<td>103646 +/- 4515</td>
-<td>74887 +/- 6080</td>
-<td>290 +/- 17</td>
-<td>99.34 +/- 3.52</td>
-<td>72.22 +/- 4.63</td>
-<td>89.19 +/- 0.59</td>
-<td>14.16 +/- 0.63</td>
-<td>0.94 +/- 0.17</td>
-</tr>
-<tr>
-<td>2</td>
-<td>289563</td>
-<td>106678 +/- 4652</td>
-<td>78260 +/- 2539</td>
-<td>294 +/- 16</td>
-<td>98.23 +/- 2.66</td>
-<td>73.43 +/- 2.52</td>
-<td>87.05 +/- 0.64</td>
-<td>16.81 +/- 0.55</td>
-<td>0.92 +/- 0.17</td>
-</tr>
-<tr>
-<td>3</td>
-<td>259242</td>
-<td>84583 +/- 5963</td>
-<td>70065 +/- 4194</td>
-<td>284 +/- 18</td>
-<td>99.82 +/- 3.05</td>
-<td>82.90 +/- 1.32</td>
-<td>89.49 +/- 0.20</td>
-<td>18.13 +/- 0.66</td>
-<td>0.81 +/- 0.13</td>
-</tr>
-<tr>
-<td>4</td>
-<td>210549</td>
-<td>68813 +/- 4782</td>
-<td>56905 +/- 4145</td>
-<td>300 +/- 29</td>
-<td>102.00 +/- 14.74</td>
-<td>82.91 +/- 5.89</td>
-<td>56.93 +/- 0.82</td>
-<td>25.85 +/- 2.30</td>
-<td>0.95 +/- 0.30</td>
-</tr>
-<tr>
-<td>5</td>
-<td>295555</td>
-<td>104854 +/- 4664</td>
-<td>79879 +/- 6270</td>
-<td>281 +/- 19</td>
-<td>98.26 +/- 5.85</td>
-<td>76.34 +/- 6.67</td>
-<td>57.71 +/- 0.30</td>
-<td>26.16 +/- 1.68</td>
-<td>0.97 +/- 0.19</td>
-</tr>
-<tr>
-<td>6</td>
-<td>140401</td>
-<td>43555 +/- 1632</td>
-<td>37946 +/- 2140</td>
-<td>233 +/- 16</td>
-<td>105.74 +/- 8.40</td>
-<td>87.14 +/- 3.87</td>
-<td>89.08 +/- 1.00</td>
-<td>33.53 +/- 2.18</td>
-<td>1.05 +/- 0.21</td>
-</tr>
-<tr>
-<td>7</td>
-<td>154217</td>
-<td>54265 +/- 1588</td>
-<td>41680 +/- 5319</td>
-<td>224 +/- 18</td>
-<td>111.33 +/- 8.90</td>
-<td>76.94 +/- 10.52</td>
-<td>84.50 +/- 1.41</td>
-<td>27.44 +/- 2.33</td>
-<td>1.32 +/- 0.25</td>
-</tr>
-<tr>
-<td>8</td>
-<td>147969</td>
-<td>64363 +/- 2697</td>
-<td>39991 +/- 6785</td>
-<td>248 +/- 43</td>
-<td>109.93 +/- 7.80</td>
-<td>62.45 +/- 12.05</td>
-<td>82.20 +/- 2.08</td>
-<td>24.63 +/- 2.53</td>
-<td>1.57 +/- 0.22</td>
-</tr>
-<tr><td colspan="13">Tile mean across chip</td></tr>
-<tr>
-<td>Av.</td>
-<td></td>
-<td>78844</td>
-<td>59952</td>
-<td>269</td>
-<td>103.08</td>
-<td>76.79</td>
-<td>79.52</td>
-<td>23.34</td>
-<td>1.06</td>
-</tr>
-</table>
-<h2><br></br>Lane Results Summary : Read 2<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>277083</td>
-<td>103647 +/- 4516</td>
-<td>74887 +/- 6080</td>
-<td>277 +/- 17</td>
-<td>94.42 +/- 5.68</td>
-<td>72.22 +/- 4.63</td>
-<td>81.54 +/- 2.13</td>
-<td>42.70 +/- 5.49</td>
-<td>0.89 +/- 0.27</td>
-</tr>
-<tr>
-<td>2</td>
-<td>289563</td>
-<td>106679 +/- 4653</td>
-<td>78260 +/- 2539</td>
-<td>259 +/- 13</td>
-<td>93.57 +/- 2.55</td>
-<td>73.43 +/- 2.52</td>
-<td>82.05 +/- 0.37</td>
-<td>43.98 +/- 3.02</td>
-<td>0.76 +/- 0.15</td>
-</tr>
-<tr>
-<td>3</td>
-<td>259242</td>
-<td>84584 +/- 5964</td>
-<td>70065 +/- 4194</td>
-<td>252 +/- 12</td>
-<td>94.23 +/- 2.19</td>
-<td>82.90 +/- 1.32</td>
-<td>84.94 +/- 0.28</td>
-<td>51.76 +/- 2.29</td>
-<td>0.59 +/- 0.07</td>
-</tr>
-<tr>
-<td>4</td>
-<td>210549</td>
-<td>68814 +/- 4783</td>
-<td>56905 +/- 4145</td>
-<td>226 +/- 16</td>
-<td>96.82 +/- 7.12</td>
-<td>82.91 +/- 5.89</td>
-<td>56.01 +/- 0.99</td>
-<td>27.86 +/- 3.48</td>
-<td>0.95 +/- 0.33</td>
-</tr>
-<tr>
-<td>5</td>
-<td>295555</td>
-<td>104855 +/- 4665</td>
-<td>79879 +/- 6270</td>
-<td>200 +/- 24</td>
-<td>103.56 +/- 15.45</td>
-<td>76.34 +/- 6.67</td>
-<td>56.76 +/- 0.41</td>
-<td>25.68 +/- 2.06</td>
-<td>0.98 +/- 0.17</td>
-</tr>
-<tr>
-<td>6</td>
-<td>140401</td>
-<td>43556 +/- 1633</td>
-<td>37946 +/- 2140</td>
-<td>179 +/- 10</td>
-<td>100.82 +/- 5.47</td>
-<td>87.14 +/- 3.87</td>
-<td>88.64 +/- 1.42</td>
-<td>34.05 +/- 2.60</td>
-<td>0.98 +/- 0.22</td>
-</tr>
-<tr>
-<td>7</td>
-<td>154217</td>
-<td>54266 +/- 1589</td>
-<td>41680 +/- 5319</td>
-<td>184 +/- 5</td>
-<td>103.42 +/- 3.47</td>
-<td>76.94 +/- 10.52</td>
-<td>83.90 +/- 1.32</td>
-<td>27.60 +/- 2.07</td>
-<td>1.26 +/- 0.16</td>
-</tr>
-<tr>
-<td>8</td>
-<td>147969</td>
-<td>64364 +/- 2698</td>
-<td>39991 +/- 6785</td>
-<td>206 +/- 31</td>
-<td>99.48 +/- 3.23</td>
-<td>62.45 +/- 12.05</td>
-<td>79.81 +/- 3.35</td>
-<td>23.06 +/- 2.50</td>
-<td>1.56 +/- 0.23</td>
-</tr>
-<tr><td colspan="13">Tile mean across chip</td></tr>
-<tr>
-<td>Av.</td>
-<td></td>
-<td>78844</td>
-<td>59952</td>
-<td>223</td>
-<td>98.29</td>
-<td>76.79</td>
-<td>76.70</td>
-<td>34.59</td>
-<td>1.00</td>
-</tr>
-</table>
-<h2><br></br>Expanded Lane Summary : Read 1<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>103646</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.37</td>
-<td>74813</td>
-<td>72.22</td>
-<td>266 +/- 17</td>
-<td>-0.53 +/- 0.37</td>
-<td>-0.42 +/- 0.21</td>
-<td>89.19</td>
-<td>0.94</td>
-<td>64718</td>
-</tr>
-<tr>
-<td>2</td>
-<td>106678</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.34</td>
-<td>74842</td>
-<td>73.43</td>
-<td>284 +/- 16</td>
-<td>0.08 +/- 0.43</td>
-<td>-0.17 +/- 0.34</td>
-<td>87.05</td>
-<td>0.92</td>
-<td>65850</td>
-</tr>
-<tr>
-<td>3</td>
-<td>84583</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.09</td>
-<td>65493</td>
-<td>82.90</td>
-<td>286 +/- 14</td>
-<td>0.29 +/- 0.48</td>
-<td>-0.02 +/- 0.17</td>
-<td>89.49</td>
-<td>0.81</td>
-<td>60899</td>
-</tr>
-<tr>
-<td>4</td>
-<td>68813</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.19</td>
-<td>33697</td>
-<td>82.91</td>
-<td>286 +/- 23</td>
-<td>-0.01 +/- 0.62</td>
-<td>-0.37 +/- 0.30</td>
-<td>56.93</td>
-<td>0.95</td>
-<td>31080</td>
-</tr>
-<tr>
-<td>5</td>
-<td>104854</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.32</td>
-<td>50075</td>
-<td>76.34</td>
-<td>258 +/- 25</td>
-<td>-0.03 +/- 0.46</td>
-<td>-0.49 +/- 0.27</td>
-<td>57.71</td>
-<td>0.97</td>
-<td>44149</td>
-</tr>
-<tr>
-<td>6</td>
-<td>43555</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.24</td>
-<td>34399</td>
-<td>87.14</td>
-<td>231 +/- 14</td>
-<td>-0.19 +/- 0.46</td>
-<td>-0.34 +/- 0.40</td>
-<td>89.08</td>
-<td>1.05</td>
-<td>32302</td>
-</tr>
-<tr>
-<td>7</td>
-<td>54265</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>1.67</td>
-<td>38188</td>
-<td>76.94</td>
-<td>224 +/- 14</td>
-<td>-0.41 +/- 0.49</td>
-<td>-0.55 +/- 0.23</td>
-<td>84.50</td>
-<td>1.32</td>
-<td>33435</td>
-</tr>
-<tr>
-<td>8</td>
-<td>64363</td>
-<td>0.8600</td>
-<td>0.4900</td>
-<td>2.15</td>
-<td>38077</td>
-<td>62.45</td>
-<td>247 +/- 42</td>
-<td>-0.52 +/- 0.36</td>
-<td>-0.29 +/- 0.19</td>
-<td>82.20</td>
-<td>1.57</td>
-<td>31036</td>
-</tr>
-</table>
-<h2><br></br>Expanded Lane Summary : Read 2<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>103646</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>1.24</td>
-<td>68870</td>
-<td>72.22</td>
-<td>254 +/- 15</td>
-<td>-0.53 +/- 0.37</td>
-<td>-0.42 +/- 0.21</td>
-<td>81.54</td>
-<td>0.89</td>
-<td>59272</td>
-</tr>
-<tr>
-<td>2</td>
-<td>106678</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>1.11</td>
-<td>71980</td>
-<td>73.43</td>
-<td>247 +/- 12</td>
-<td>0.08 +/- 0.43</td>
-<td>-0.17 +/- 0.34</td>
-<td>82.05</td>
-<td>0.76</td>
-<td>62240</td>
-</tr>
-<tr>
-<td>3</td>
-<td>84583</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>0.80</td>
-<td>63500</td>
-<td>82.90</td>
-<td>243 +/- 8</td>
-<td>0.29 +/- 0.48</td>
-<td>-0.02 +/- 0.17</td>
-<td>84.94</td>
-<td>0.59</td>
-<td>58029</td>
-</tr>
-<tr>
-<td>4</td>
-<td>68813</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>1.12</td>
-<td>33534</td>
-<td>82.91</td>
-<td>210 +/- 19</td>
-<td>-0.01 +/- 0.62</td>
-<td>-0.37 +/- 0.30</td>
-<td>56.01</td>
-<td>0.95</td>
-<td>30548</td>
-</tr>
-<tr>
-<td>5</td>
-<td>104854</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>1.24</td>
-<td>49951</td>
-<td>76.34</td>
-<td>193 +/- 12</td>
-<td>-0.03 +/- 0.46</td>
-<td>-0.49 +/- 0.27</td>
-<td>56.76</td>
-<td>0.98</td>
-<td>43366</td>
-</tr>
-<tr>
-<td>6</td>
-<td>43555</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>1.12</td>
-<td>34751</td>
-<td>87.14</td>
-<td>174 +/- 7</td>
-<td>-0.19 +/- 0.46</td>
-<td>-0.34 +/- 0.40</td>
-<td>88.64</td>
-<td>0.98</td>
-<td>32208</td>
-</tr>
-<tr>
-<td>7</td>
-<td>54265</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>1.55</td>
-<td>38418</td>
-<td>76.94</td>
-<td>178 +/- 4</td>
-<td>-0.41 +/- 0.49</td>
-<td>-0.55 +/- 0.23</td>
-<td>83.90</td>
-<td>1.26</td>
-<td>33240</td>
-</tr>
-<tr>
-<td>8</td>
-<td>64363</td>
-<td>0.7900</td>
-<td>0.4600</td>
-<td>2.07</td>
-<td>36968</td>
-<td>62.45</td>
-<td>198 +/- 32</td>
-<td>-0.52 +/- 0.36</td>
-<td>-0.29 +/- 0.19</td>
-<td>79.81</td>
-<td>1.56</td>
-<td>30181</td>
-</tr>
-</table>
-</body>
-</html>"""
- pathname = os.path.join(gerald_dir, 'Summary.htm')
- f = open(pathname, 'w')
- f.write(summary_htm)
- f.close()
+ source = os.path.join(TESTDATA_DIR, 'Summary-paired-pipeline110.htm')
+ destination = os.path.join(gerald_dir, 'Summary.htm')
+ shutil.copy(source, destination)
def make_summary_ipar130_htm(gerald_dir):
- test_dir = os.path.split(__file__)[0]
- testdata_dir = os.path.join(test_dir, 'testdata')
- summary_htm = os.path.join(testdata_dir, 'Summary-ipar130.htm')
- dest = os.path.join(gerald_dir, 'Summary.htm')
- shutil.copy(summary_htm, dest)
+ source = os.path.join(TESTDATA_DIR, 'Summary-ipar130.htm')
+ destination = os.path.join(gerald_dir, 'Summary.htm')
+ shutil.copy(source, destination)
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.
os.mkdir(self.firecrest_dir)
self.matrix_dir = os.path.join(self.firecrest_dir, 'Matrix')
os.mkdir(self.matrix_dir)
- make_matrix(self.matrix_dir)
+ matrix_filename = os.path.join(self.matrix_dir, 's_matrix')
+ make_matrix(matrix_filename)
self.bustard_dir = os.path.join(self.firecrest_dir,
'Bustard1.8.28_12-04-2008_diane')
self.gerald_dir = os.path.join(self.bustard_dir,
'GERALD_12-04-2008_diane')
os.mkdir(self.gerald_dir)
- make_gerald_config(self.gerald_dir)
+ make_gerald_config_026(self.gerald_dir)
make_summary_htm(self.gerald_dir)
make_eland_results(self.gerald_dir)
os.mkdir(firecrest_dir)
matrix_dir = os.path.join(firecrest_dir, 'Matrix')
os.mkdir(matrix_dir)
- make_matrix(matrix_dir)
+ matrix_filename = os.path.join(matrix_dir, 's_matrix.txt')
+ make_matrix(matrix_filename)
bustard_dir = os.path.join(firecrest_dir,
'Bustard1.8.28_12-04-2008_diane')
gerald_dir = os.path.join(bustard_dir,
'GERALD_12-04-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
+ make_gerald_config_026(gerald_dir)
make_summary_htm(gerald_dir)
make_eland_results(gerald_dir)
'C1-37_Firecrest1.9.6_20-10-2008_diane')
os.mkdir(firecrest_dir)
- matrix_dir = os.path.join(firecrest_dir, 'Matrix')
- os.mkdir(matrix_dir)
- make_matrix(matrix_dir)
-
bustard_dir = os.path.join(firecrest_dir,
'Bustard1.9.6_20-10-2008_diane')
os.mkdir(bustard_dir)
make_phasing_params(bustard_dir)
+ matrix_name = os.path.join(bustard_dir, 'matrix1.txt')
+ make_matrix(matrix_name)
+
+
gerald_dir = os.path.join(bustard_dir,
'GERALD_20-10-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
+ make_gerald_config_100(gerald_dir)
make_summary_htm_110(gerald_dir)
make_eland_multi(gerald_dir)
obj.runfolder_dir = runfolder_dir
obj.data_dir = data_dir
obj.image_analysis_dir = firecrest_dir
- obj.matrix_dir = matrix_dir
obj.bustard_dir = bustard_dir
obj.gerald_dir = gerald_dir
g = gerald.gerald(self.gerald_dir)
self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
- self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
+ '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+ self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
# instead of pythons default 0..8
- genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
- '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
+ genomes = [None,
+ '/g/mm9',
+ '/g/mm9',
+ '/g/elegans190',
+ '/g/arabidopsis01222004',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9', ]
# test lane specific parameters from gerald config file
for i in range(1,9):
cur_lane = g.lanes[i]
- self.failUnlessEqual(cur_lane.analysis, 'eland')
+ self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
- self.failUnlessEqual(cur_lane.read_length, '32')
- self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+ self.failUnlessEqual(cur_lane.read_length, '37')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
# I want to be able to use a simple iterator
for l in g.lanes.values():
- self.failUnlessEqual(l.analysis, 'eland')
- self.failUnlessEqual(l.read_length, '32')
- self.failUnlessEqual(l.use_bases, 'Y'*32)
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
# raw cluster numbers extracted from summary file
# its the first +/- value in the lane results summary
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
- name = 'run_30J55AAXX_2008-10-20.xml'
+ name = 'run_30J55AAXX_2009-02-22.xml'
self.failUnlessEqual(runs[0].name, name)
# do we get the flowcell id from the FlowcellId.xml file
make_flowcell_id(self.runfolder_dir, '30J55AAXX')
runs = runfolder.get_runs(self.runfolder_dir)
self.failUnlessEqual(len(runs), 1)
- name = 'run_30J55AAXX_2008-10-20.xml'
+ name = 'run_30J55AAXX_2009-02-22.xml'
self.failUnlessEqual(runs[0].name, name)
r1 = runs[0]
matrix_dir = os.path.join(ipar_dir, 'Matrix')
os.mkdir(matrix_dir)
- make_matrix(matrix_dir)
+ matrix_name = os.path.join(matrix_dir, 's_matrix.txt')
+ make_matrix(matrix_name)
bustard_dir = os.path.join(ipar_dir,
'Bustard1.8.28_12-04-2008_diane')
gerald_dir = os.path.join(bustard_dir,
'GERALD_12-04-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
- make_summary100_htm(gerald_dir)
+ make_gerald_config_100(gerald_dir)
+ make_summary_htm_100(gerald_dir)
make_eland_multi(gerald_dir)
if obj is not None:
g = gerald.gerald(self.gerald_dir)
self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
- self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
+ '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+ self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
# instead of pythons default 0..8
- genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
- '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
+ genomes = [None,
+ '/g/mm9',
+ '/g/mm9',
+ '/g/elegans190',
+ '/g/arabidopsis01222004',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9', ]
# test lane specific parameters from gerald config file
for i in range(1,9):
cur_lane = g.lanes[i]
- self.failUnlessEqual(cur_lane.analysis, 'eland')
+ self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
- self.failUnlessEqual(cur_lane.read_length, '32')
- self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+ self.failUnlessEqual(cur_lane.read_length, '37')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
# I want to be able to use a simple iterator
for l in g.lanes.values():
- self.failUnlessEqual(l.analysis, 'eland')
- self.failUnlessEqual(l.read_length, '32')
- self.failUnlessEqual(l.use_bases, 'Y'*32)
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
# test data extracted from summary file
clusters = [None,
gerald_dir = os.path.join(bustard_dir,
'GERALD_15-03-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
+ make_gerald_config_100(gerald_dir)
make_summary_ipar130_htm(gerald_dir)
make_eland_multi(gerald_dir)
g = gerald.gerald(self.gerald_dir)
self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
- self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
+ '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+ self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
# instead of pythons default 0..8
- genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
- '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
+ genomes = [None,
+ '/g/mm9',
+ '/g/mm9',
+ '/g/elegans190',
+ '/g/arabidopsis01222004',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9', ]
# test lane specific parameters from gerald config file
for i in range(1,9):
cur_lane = g.lanes[i]
- self.failUnlessEqual(cur_lane.analysis, 'eland')
+ self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
- self.failUnlessEqual(cur_lane.read_length, '32')
- self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+ self.failUnlessEqual(cur_lane.read_length, '37')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
# I want to be able to use a simple iterator
for l in g.lanes.values():
- self.failUnlessEqual(l.analysis, 'eland')
- self.failUnlessEqual(l.read_length, '32')
- self.failUnlessEqual(l.use_bases, 'Y'*32)
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
# test data extracted from summary file
clusters = [None,
matrix_dir = os.path.join(ipar_dir, 'Matrix')
os.mkdir(matrix_dir)
- make_matrix(matrix_dir)
+ matrix_name = os.path.join(matrix_dir, 's_matrix.txt')
+ make_matrix(matrix_name)
bustard_dir = os.path.join(ipar_dir,
'Bustard1.8.28_12-04-2008_diane')
gerald_dir = os.path.join(bustard_dir,
'GERALD_12-04-2008_diane')
os.mkdir(gerald_dir)
- make_gerald_config(gerald_dir)
+ make_gerald_config_100(gerald_dir)
make_summary_paired_htm(gerald_dir)
make_eland_multi(gerald_dir, paired=True)
g = gerald.gerald(self.gerald_dir)
self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
- self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
+ '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
+ self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
# make_gerald_config.
# the first None is to offset the genomes list to be 1..9
# instead of pythons default 0..8
- genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
- '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
+ genomes = [None,
+ '/g/mm9',
+ '/g/mm9',
+ '/g/elegans190',
+ '/g/arabidopsis01222004',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9', ]
# test lane specific parameters from gerald config file
for i in range(1,9):
cur_lane = g.lanes[i]
- self.failUnlessEqual(cur_lane.analysis, 'eland')
+ self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
- self.failUnlessEqual(cur_lane.read_length, '32')
- self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+ self.failUnlessEqual(cur_lane.read_length, '37')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
# I want to be able to use a simple iterator
for l in g.lanes.values():
- self.failUnlessEqual(l.analysis, 'eland')
- self.failUnlessEqual(l.read_length, '32')
- self.failUnlessEqual(l.use_bases, 'Y'*32)
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
# test data extracted from summary file
clusters = [[None,
# do we get the flowcell id from the filename?
self.failUnlessEqual(len(runs), 1)
# firecrest's date depends on filename not the create time.
- name = 'run_207BTAAXX_2008-04-19.xml'
+ name = 'run_207BTAAXX_2009-02-22.xml'
self.failUnlessEqual(runs[0].name, name)
# do we get the flowcell id from the FlowcellId.xml file
make_flowcell_id(self.runfolder_dir, '207BTAAXY')
runs = runfolder.get_runs(self.runfolder_dir)
self.failUnlessEqual(len(runs), 1)
- name = 'run_207BTAAXY_2008-04-19.xml'
+ name = 'run_207BTAAXY_2009-02-22.xml'
self.failUnlessEqual(runs[0].name, name)
r1 = runs[0]
--- /dev/null
+<?xml version="1.0"?>\r
+<ImageAnalysis>\r
+ <Run Name="IPAR_1.01">\r
+ <Software Name="IPAR" Version="2.01.192.0" />\r
+ <Cycles First="1" Last="37" Number="37" />\r
+ <RunParameters>\r
+ <ImagingReads Index="1">\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>37</LastCycle>\r
+ <RunFolder>090220_HWI-EAS229_0093_30VR0AAXX</RunFolder>\r
+ </ImagingReads>\r
+ <Reads Index="1">\r
+ <FirstCycle>1</FirstCycle>\r
+ <LastCycle>37</LastCycle>\r
+ <RunFolder>090220_HWI-EAS229_0093_30VR0AAXX</RunFolder>\r
+ </Reads>\r
+ <Compression>gzip</Compression>\r
+ <CompressionSuffix>.p.gz</CompressionSuffix>\r
+ <Instrument>HWI-EAS229</Instrument>\r
+ <RunFolder>090220_HWI-EAS229_0093_30VR0AAXX</RunFolder>\r
+ </RunParameters>\r
+ <ImageParameters>\r
+ <AutoOffsetFlag>1</AutoOffsetFlag>\r
+ <Fwhm>2.7</Fwhm>\r
+ <RemappingDistance>1.5</RemappingDistance>\r
+ <Threshold>4</Threshold>\r
+ </ImageParameters>\r
+ <TileSelection>\r
+ <Lane Index="1">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="2">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="3">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="4">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="5">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="6">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="7">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ <Lane Index="8">\r
+ <Sample>s</Sample>\r
+ <TileRange Max="100" Min="1" />\r
+ </Lane>\r
+ </TileSelection>\r
+ </Run>\r
+</ImageAnalysis>
\ No newline at end of file
--- /dev/null
+<!--RUN_TIME Thu Nov 13 15:11:29 2008 -->
+<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
+<html>
+<body>
+
+<a name="Top"><h2><title>080920_HWI-EAS229_0057_30GBJAAXX Summary</title></h2></a>
+<h1>Summary Information For Experiment 080920_HWI-EAS229_0057_30GBJAAXX on Machine unknown</h1>
+<h2><br></br>Chip Summary<br></br></h2>
+<table border="1" cellpadding="5">
+<tr><td>Machine</td><td>UNKNOWN</td></tr>
+<tr><td>Run Folder</td><td>080920_HWI-EAS229_0057_30GBJAAXX</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>126151880</td>
+<td>95923456</td>
+<td>3549167</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_PAIR</td>
+<td>37, 37</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>hg18</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</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_PAIR</td>
+<td>37, 37</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>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</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>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</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>hg18</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</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>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</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>mm9</td>
+<td>ELAND_PAIR</td>
+<td>37, 37</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 : Read 1<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>277083</td>
+<td>103646 +/- 4515</td>
+<td>74887 +/- 6080</td>
+<td>290 +/- 17</td>
+<td>99.34 +/- 3.52</td>
+<td>72.22 +/- 4.63</td>
+<td>89.19 +/- 0.59</td>
+<td>14.16 +/- 0.63</td>
+<td>0.94 +/- 0.17</td>
+</tr>
+<tr>
+<td>2</td>
+<td>289563</td>
+<td>106678 +/- 4652</td>
+<td>78260 +/- 2539</td>
+<td>294 +/- 16</td>
+<td>98.23 +/- 2.66</td>
+<td>73.43 +/- 2.52</td>
+<td>87.05 +/- 0.64</td>
+<td>16.81 +/- 0.55</td>
+<td>0.92 +/- 0.17</td>
+</tr>
+<tr>
+<td>3</td>
+<td>259242</td>
+<td>84583 +/- 5963</td>
+<td>70065 +/- 4194</td>
+<td>284 +/- 18</td>
+<td>99.82 +/- 3.05</td>
+<td>82.90 +/- 1.32</td>
+<td>89.49 +/- 0.20</td>
+<td>18.13 +/- 0.66</td>
+<td>0.81 +/- 0.13</td>
+</tr>
+<tr>
+<td>4</td>
+<td>210549</td>
+<td>68813 +/- 4782</td>
+<td>56905 +/- 4145</td>
+<td>300 +/- 29</td>
+<td>102.00 +/- 14.74</td>
+<td>82.91 +/- 5.89</td>
+<td>56.93 +/- 0.82</td>
+<td>25.85 +/- 2.30</td>
+<td>0.95 +/- 0.30</td>
+</tr>
+<tr>
+<td>5</td>
+<td>295555</td>
+<td>104854 +/- 4664</td>
+<td>79879 +/- 6270</td>
+<td>281 +/- 19</td>
+<td>98.26 +/- 5.85</td>
+<td>76.34 +/- 6.67</td>
+<td>57.71 +/- 0.30</td>
+<td>26.16 +/- 1.68</td>
+<td>0.97 +/- 0.19</td>
+</tr>
+<tr>
+<td>6</td>
+<td>140401</td>
+<td>43555 +/- 1632</td>
+<td>37946 +/- 2140</td>
+<td>233 +/- 16</td>
+<td>105.74 +/- 8.40</td>
+<td>87.14 +/- 3.87</td>
+<td>89.08 +/- 1.00</td>
+<td>33.53 +/- 2.18</td>
+<td>1.05 +/- 0.21</td>
+</tr>
+<tr>
+<td>7</td>
+<td>154217</td>
+<td>54265 +/- 1588</td>
+<td>41680 +/- 5319</td>
+<td>224 +/- 18</td>
+<td>111.33 +/- 8.90</td>
+<td>76.94 +/- 10.52</td>
+<td>84.50 +/- 1.41</td>
+<td>27.44 +/- 2.33</td>
+<td>1.32 +/- 0.25</td>
+</tr>
+<tr>
+<td>8</td>
+<td>147969</td>
+<td>64363 +/- 2697</td>
+<td>39991 +/- 6785</td>
+<td>248 +/- 43</td>
+<td>109.93 +/- 7.80</td>
+<td>62.45 +/- 12.05</td>
+<td>82.20 +/- 2.08</td>
+<td>24.63 +/- 2.53</td>
+<td>1.57 +/- 0.22</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>78844</td>
+<td>59952</td>
+<td>269</td>
+<td>103.08</td>
+<td>76.79</td>
+<td>79.52</td>
+<td>23.34</td>
+<td>1.06</td>
+</tr>
+</table>
+<h2><br></br>Lane Results Summary : Read 2<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>277083</td>
+<td>103647 +/- 4516</td>
+<td>74887 +/- 6080</td>
+<td>277 +/- 17</td>
+<td>94.42 +/- 5.68</td>
+<td>72.22 +/- 4.63</td>
+<td>81.54 +/- 2.13</td>
+<td>42.70 +/- 5.49</td>
+<td>0.89 +/- 0.27</td>
+</tr>
+<tr>
+<td>2</td>
+<td>289563</td>
+<td>106679 +/- 4653</td>
+<td>78260 +/- 2539</td>
+<td>259 +/- 13</td>
+<td>93.57 +/- 2.55</td>
+<td>73.43 +/- 2.52</td>
+<td>82.05 +/- 0.37</td>
+<td>43.98 +/- 3.02</td>
+<td>0.76 +/- 0.15</td>
+</tr>
+<tr>
+<td>3</td>
+<td>259242</td>
+<td>84584 +/- 5964</td>
+<td>70065 +/- 4194</td>
+<td>252 +/- 12</td>
+<td>94.23 +/- 2.19</td>
+<td>82.90 +/- 1.32</td>
+<td>84.94 +/- 0.28</td>
+<td>51.76 +/- 2.29</td>
+<td>0.59 +/- 0.07</td>
+</tr>
+<tr>
+<td>4</td>
+<td>210549</td>
+<td>68814 +/- 4783</td>
+<td>56905 +/- 4145</td>
+<td>226 +/- 16</td>
+<td>96.82 +/- 7.12</td>
+<td>82.91 +/- 5.89</td>
+<td>56.01 +/- 0.99</td>
+<td>27.86 +/- 3.48</td>
+<td>0.95 +/- 0.33</td>
+</tr>
+<tr>
+<td>5</td>
+<td>295555</td>
+<td>104855 +/- 4665</td>
+<td>79879 +/- 6270</td>
+<td>200 +/- 24</td>
+<td>103.56 +/- 15.45</td>
+<td>76.34 +/- 6.67</td>
+<td>56.76 +/- 0.41</td>
+<td>25.68 +/- 2.06</td>
+<td>0.98 +/- 0.17</td>
+</tr>
+<tr>
+<td>6</td>
+<td>140401</td>
+<td>43556 +/- 1633</td>
+<td>37946 +/- 2140</td>
+<td>179 +/- 10</td>
+<td>100.82 +/- 5.47</td>
+<td>87.14 +/- 3.87</td>
+<td>88.64 +/- 1.42</td>
+<td>34.05 +/- 2.60</td>
+<td>0.98 +/- 0.22</td>
+</tr>
+<tr>
+<td>7</td>
+<td>154217</td>
+<td>54266 +/- 1589</td>
+<td>41680 +/- 5319</td>
+<td>184 +/- 5</td>
+<td>103.42 +/- 3.47</td>
+<td>76.94 +/- 10.52</td>
+<td>83.90 +/- 1.32</td>
+<td>27.60 +/- 2.07</td>
+<td>1.26 +/- 0.16</td>
+</tr>
+<tr>
+<td>8</td>
+<td>147969</td>
+<td>64364 +/- 2698</td>
+<td>39991 +/- 6785</td>
+<td>206 +/- 31</td>
+<td>99.48 +/- 3.23</td>
+<td>62.45 +/- 12.05</td>
+<td>79.81 +/- 3.35</td>
+<td>23.06 +/- 2.50</td>
+<td>1.56 +/- 0.23</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>78844</td>
+<td>59952</td>
+<td>223</td>
+<td>98.29</td>
+<td>76.79</td>
+<td>76.70</td>
+<td>34.59</td>
+<td>1.00</td>
+</tr>
+</table>
+<h2><br></br>Expanded Lane Summary : Read 1<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>103646</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.37</td>
+<td>74813</td>
+<td>72.22</td>
+<td>266 +/- 17</td>
+<td>-0.53 +/- 0.37</td>
+<td>-0.42 +/- 0.21</td>
+<td>89.19</td>
+<td>0.94</td>
+<td>64718</td>
+</tr>
+<tr>
+<td>2</td>
+<td>106678</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.34</td>
+<td>74842</td>
+<td>73.43</td>
+<td>284 +/- 16</td>
+<td>0.08 +/- 0.43</td>
+<td>-0.17 +/- 0.34</td>
+<td>87.05</td>
+<td>0.92</td>
+<td>65850</td>
+</tr>
+<tr>
+<td>3</td>
+<td>84583</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.09</td>
+<td>65493</td>
+<td>82.90</td>
+<td>286 +/- 14</td>
+<td>0.29 +/- 0.48</td>
+<td>-0.02 +/- 0.17</td>
+<td>89.49</td>
+<td>0.81</td>
+<td>60899</td>
+</tr>
+<tr>
+<td>4</td>
+<td>68813</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.19</td>
+<td>33697</td>
+<td>82.91</td>
+<td>286 +/- 23</td>
+<td>-0.01 +/- 0.62</td>
+<td>-0.37 +/- 0.30</td>
+<td>56.93</td>
+<td>0.95</td>
+<td>31080</td>
+</tr>
+<tr>
+<td>5</td>
+<td>104854</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.32</td>
+<td>50075</td>
+<td>76.34</td>
+<td>258 +/- 25</td>
+<td>-0.03 +/- 0.46</td>
+<td>-0.49 +/- 0.27</td>
+<td>57.71</td>
+<td>0.97</td>
+<td>44149</td>
+</tr>
+<tr>
+<td>6</td>
+<td>43555</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.24</td>
+<td>34399</td>
+<td>87.14</td>
+<td>231 +/- 14</td>
+<td>-0.19 +/- 0.46</td>
+<td>-0.34 +/- 0.40</td>
+<td>89.08</td>
+<td>1.05</td>
+<td>32302</td>
+</tr>
+<tr>
+<td>7</td>
+<td>54265</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>1.67</td>
+<td>38188</td>
+<td>76.94</td>
+<td>224 +/- 14</td>
+<td>-0.41 +/- 0.49</td>
+<td>-0.55 +/- 0.23</td>
+<td>84.50</td>
+<td>1.32</td>
+<td>33435</td>
+</tr>
+<tr>
+<td>8</td>
+<td>64363</td>
+<td>0.8600</td>
+<td>0.4900</td>
+<td>2.15</td>
+<td>38077</td>
+<td>62.45</td>
+<td>247 +/- 42</td>
+<td>-0.52 +/- 0.36</td>
+<td>-0.29 +/- 0.19</td>
+<td>82.20</td>
+<td>1.57</td>
+<td>31036</td>
+</tr>
+</table>
+<h2><br></br>Expanded Lane Summary : Read 2<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>103646</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.24</td>
+<td>68870</td>
+<td>72.22</td>
+<td>254 +/- 15</td>
+<td>-0.53 +/- 0.37</td>
+<td>-0.42 +/- 0.21</td>
+<td>81.54</td>
+<td>0.89</td>
+<td>59272</td>
+</tr>
+<tr>
+<td>2</td>
+<td>106678</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.11</td>
+<td>71980</td>
+<td>73.43</td>
+<td>247 +/- 12</td>
+<td>0.08 +/- 0.43</td>
+<td>-0.17 +/- 0.34</td>
+<td>82.05</td>
+<td>0.76</td>
+<td>62240</td>
+</tr>
+<tr>
+<td>3</td>
+<td>84583</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>0.80</td>
+<td>63500</td>
+<td>82.90</td>
+<td>243 +/- 8</td>
+<td>0.29 +/- 0.48</td>
+<td>-0.02 +/- 0.17</td>
+<td>84.94</td>
+<td>0.59</td>
+<td>58029</td>
+</tr>
+<tr>
+<td>4</td>
+<td>68813</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.12</td>
+<td>33534</td>
+<td>82.91</td>
+<td>210 +/- 19</td>
+<td>-0.01 +/- 0.62</td>
+<td>-0.37 +/- 0.30</td>
+<td>56.01</td>
+<td>0.95</td>
+<td>30548</td>
+</tr>
+<tr>
+<td>5</td>
+<td>104854</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.24</td>
+<td>49951</td>
+<td>76.34</td>
+<td>193 +/- 12</td>
+<td>-0.03 +/- 0.46</td>
+<td>-0.49 +/- 0.27</td>
+<td>56.76</td>
+<td>0.98</td>
+<td>43366</td>
+</tr>
+<tr>
+<td>6</td>
+<td>43555</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.12</td>
+<td>34751</td>
+<td>87.14</td>
+<td>174 +/- 7</td>
+<td>-0.19 +/- 0.46</td>
+<td>-0.34 +/- 0.40</td>
+<td>88.64</td>
+<td>0.98</td>
+<td>32208</td>
+</tr>
+<tr>
+<td>7</td>
+<td>54265</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>1.55</td>
+<td>38418</td>
+<td>76.94</td>
+<td>178 +/- 4</td>
+<td>-0.41 +/- 0.49</td>
+<td>-0.55 +/- 0.23</td>
+<td>83.90</td>
+<td>1.26</td>
+<td>33240</td>
+</tr>
+<tr>
+<td>8</td>
+<td>64363</td>
+<td>0.7900</td>
+<td>0.4600</td>
+<td>2.07</td>
+<td>36968</td>
+<td>62.45</td>
+<td>198 +/- 32</td>
+<td>-0.52 +/- 0.36</td>
+<td>-0.29 +/- 0.19</td>
+<td>79.81</td>
+<td>1.56</td>
+<td>30181</td>
+</tr>
+</table>
+</body>
+</html>
\ No newline at end of file
--- /dev/null
+<!--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>
--- /dev/null
+<!--RUN_TIME Tue Oct 28 09:45:50 2008 -->
+<!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.10 2008/07/23 15:18:30 mzerara Exp $-->
+<html>
+<body>
+
+<a name="Top"><h2><title>081017_HWI-EAS229_0062_30J55AAXX Summary</title></h2></a>
+<h1>Summary Information For Experiment 081017_HWI-EAS229_0062_30J55AAXX 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>081017_HWI-EAS229_0062_30J55AAXX</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>162491175</td>
+<td>99622159</td>
+<td>3686019</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>Chast. Thresh.</td>
+<td>Num Tiles</td>
+<td>Tiles</td>
+</tr>
+<tr>
+<td>1</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>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>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>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>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane3">Lane 3</a></td>
+</tr>
+<tr>
+<td>4</td>
+<td>unknown</td>
+<td>hg18</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane4">Lane 4</a></td>
+</tr>
+<tr>
+<td>5</td>
+<td>unknown</td>
+<td>hg18</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane5">Lane 5</a></td>
+</tr>
+<tr>
+<td>6</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane6">Lane 6</a></td>
+</tr>
+<tr>
+<td>7</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>0.6</td>
+<td>100</td>
+<td><a href="#Lane7">Lane 7</a></td>
+</tr>
+<tr>
+<td>8</td>
+<td>unknown</td>
+<td>mm9</td>
+<td>ELAND</td>
+<td>37</td>
+<td>'((FAILED_CHASTITY<=1))'</td>
+<td>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>435340</td>
+<td>190220 +/- 15118</td>
+<td>117659 +/- 8144</td>
+<td>273 +/- 16</td>
+<td>80.02 +/- 2.52</td>
+<td>62.15 +/- 5.54</td>
+<td>77.18 +/- 0.22</td>
+<td>13447.28 +/- 43.35</td>
+<td>2.78 +/- 0.13</td>
+</tr>
+<tr>
+<td>2</td>
+<td>462364</td>
+<td>190560 +/- 14399</td>
+<td>124963 +/- 5687</td>
+<td>271 +/- 16</td>
+<td>75.73 +/- 2.46</td>
+<td>65.83 +/- 4.12</td>
+<td>70.06 +/- 0.39</td>
+<td>12082.95 +/- 64.81</td>
+<td>3.22 +/- 0.09</td>
+</tr>
+<tr>
+<td>3</td>
+<td>468929</td>
+<td>187597 +/- 12369</td>
+<td>126737 +/- 5549</td>
+<td>274 +/- 16</td>
+<td>72.61 +/- 2.67</td>
+<td>67.69 +/- 2.72</td>
+<td>74.03 +/- 0.22</td>
+<td>12470.18 +/- 50.02</td>
+<td>4.27 +/- 0.08</td>
+</tr>
+<tr>
+<td>4</td>
+<td>491642</td>
+<td>204142 +/- 16877</td>
+<td>132876 +/- 4023</td>
+<td>253 +/- 16</td>
+<td>80.43 +/- 3.10</td>
+<td>65.39 +/- 3.84</td>
+<td>72.95 +/- 0.15</td>
+<td>13273.80 +/- 39.75</td>
+<td>0.78 +/- 0.10</td>
+</tr>
+<tr>
+<td>5</td>
+<td>433033</td>
+<td>247308 +/- 11600</td>
+<td>117036 +/- 4489</td>
+<td>273 +/- 11</td>
+<td>68.60 +/- 2.40</td>
+<td>47.48 +/- 3.63</td>
+<td>66.91 +/- 0.54</td>
+<td>11700.08 +/- 66.33</td>
+<td>2.62 +/- 0.13</td>
+</tr>
+<tr>
+<td>6</td>
+<td>483012</td>
+<td>204298 +/- 15640</td>
+<td>130543 +/- 6972</td>
+<td>254 +/- 11</td>
+<td>81.35 +/- 1.96</td>
+<td>64.14 +/- 4.40</td>
+<td>77.28 +/- 0.11</td>
+<td>14084.01 +/- 23.09</td>
+<td>0.71 +/- 0.03</td>
+</tr>
+<tr>
+<td>7</td>
+<td>474325</td>
+<td>202707 +/- 15404</td>
+<td>128196 +/- 9745</td>
+<td>255 +/- 13</td>
+<td>79.95 +/- 2.08</td>
+<td>63.48 +/- 5.63</td>
+<td>75.78 +/- 0.18</td>
+<td>13758.74 +/- 60.86</td>
+<td>0.88 +/- 0.12</td>
+</tr>
+<tr>
+<td>8</td>
+<td>437372</td>
+<td>198075 +/- 14702</td>
+<td>118208 +/- 14798</td>
+<td>259 +/- 14</td>
+<td>81.80 +/- 2.53</td>
+<td>59.85 +/- 7.67</td>
+<td>74.55 +/- 0.36</td>
+<td>13586.07 +/- 103.97</td>
+<td>0.71 +/- 0.15</td>
+</tr>
+<tr><td colspan="13">Tile mean across chip</td></tr>
+<tr>
+<td>Av.</td>
+<td></td>
+<td>203113</td>
+<td>124527</td>
+<td>264</td>
+<td>77.56</td>
+<td>62.00</td>
+<td>73.59</td>
+<td>13050.39</td>
+<td>2.00</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>190220</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>3.17</td>
+<td>107262</td>
+<td>62.15</td>
+<td>241 +/- 13</td>
+<td>0.56 +/- 0.22</td>
+<td>0.29 +/- 0.14</td>
+<td>77.18</td>
+<td>2.78</td>
+<td>86184</td>
+</tr>
+<tr>
+<td>2</td>
+<td>190560</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>3.53</td>
+<td>98678</td>
+<td>65.83</td>
+<td>238 +/- 14</td>
+<td>0.78 +/- 0.15</td>
+<td>0.53 +/- 0.15</td>
+<td>70.06</td>
+<td>3.22</td>
+<td>83090</td>
+</tr>
+<tr>
+<td>3</td>
+<td>187597</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>4.44</td>
+<td>104008</td>
+<td>67.69</td>
+<td>233 +/- 14</td>
+<td>0.56 +/- 0.17</td>
+<td>0.59 +/- 0.26</td>
+<td>74.03</td>
+<td>4.27</td>
+<td>89278</td>
+</tr>
+<tr>
+<td>4</td>
+<td>204142</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.38</td>
+<td>115765</td>
+<td>65.39</td>
+<td>239 +/- 14</td>
+<td>1.28 +/- 0.21</td>
+<td>0.77 +/- 0.21</td>
+<td>72.95</td>
+<td>0.78</td>
+<td>93475</td>
+</tr>
+<tr>
+<td>5</td>
+<td>247308</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>3.40</td>
+<td>103006</td>
+<td>47.48</td>
+<td>242 +/- 10</td>
+<td>1.61 +/- 0.39</td>
+<td>1.21 +/- 0.21</td>
+<td>66.91</td>
+<td>2.62</td>
+<td>73768</td>
+</tr>
+<tr>
+<td>6</td>
+<td>204298</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.33</td>
+<td>122233</td>
+<td>64.14</td>
+<td>242 +/- 12</td>
+<td>1.30 +/- 0.11</td>
+<td>0.73 +/- 0.22</td>
+<td>77.28</td>
+<td>0.71</td>
+<td>97646</td>
+</tr>
+<tr>
+<td>7</td>
+<td>202707</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.51</td>
+<td>117513</td>
+<td>63.48</td>
+<td>238 +/- 13</td>
+<td>1.27 +/- 0.38</td>
+<td>0.66 +/- 0.22</td>
+<td>75.78</td>
+<td>0.88</td>
+<td>93659</td>
+</tr>
+<tr>
+<td>8</td>
+<td>198075</td>
+<td>0.6800</td>
+<td>0.2800</td>
+<td>1.41</td>
+<td>111115</td>
+<td>59.85</td>
+<td>244 +/- 12</td>
+<td>1.19 +/- 0.16</td>
+<td>0.65 +/- 0.29</td>
+<td>74.55</td>
+<td>0.71</td>
+<td>85327</td>
+</tr>
+</table>
+</body>
+</html>
\ No newline at end of file
--- /dev/null
+<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>
--- /dev/null
+<RunParameters>
+<ChipWideRunParameters>
+ <ANALYSIS>none</ANALYSIS>
+ <BAD_LANES></BAD_LANES>
+ <BAD_LANES></BAD_LANES>
+ <BAD_LANES></BAD_LANES>
+ <BAD_TILES></BAD_TILES>
+ <BIN_DIR>/home/diane/proj/GAPipeline-1.0/Goat/../Gerald/../bin</BIN_DIR>
+ <CMDPREFIX></CMDPREFIX>
+ <CONTAM_DIR></CONTAM_DIR>
+ <CONTAM_FILE></CONTAM_FILE>
+ <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
+ <ELAND_MAX_MATCHES></ELAND_MAX_MATCHES>
+ <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
+ <ELAND_REPEAT></ELAND_REPEAT>
+ <ELAND_SEED_LENGTH></ELAND_SEED_LENGTH>
+ <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
+ <EMAIL_LIST>diane</EMAIL_LIST>
+ <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
+ <EXPT_DIR>/home/diane/gec/090220_HWI-EAS229_0093_30VR0AAXX/Data/C1-37_Firecrest1.9.5_22-02-2009_diane/Bustard1.9.5_22-02-2009_diane</EXPT_DIR>
+ <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
+ <FORCE>1</FORCE>
+ <GENOME_DIR>/home/diane/proj/GAPipeline-1.0/Goat/../Gerald/../../Genomes</GENOME_DIR>
+ <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
+ <GROUP_LANES></GROUP_LANES>
+ <HAMSTER_FLAG>genome</HAMSTER_FLAG>
+ <HAMSTER_FLAG>genome</HAMSTER_FLAG>
+ <HAMSTER_FLAG>genome</HAMSTER_FLAG>
+ <INDEX_BASES></INDEX_BASES>
+ <NUM_LEADING_DIRS_TO_STRIP>2</NUM_LEADING_DIRS_TO_STRIP>
+ <ORIG_READ_LENGTHS>37</ORIG_READ_LENGTHS>
+ <OUT_DIR>/home/diane/gec/090220_HWI-EAS229_0093_30VR0AAXX/Data/C1-37_Firecrest1.9.5_22-02-2009_diane/Bustard1.9.5_22-02-2009_diane/GERALD_22-02-2009_diane</OUT_DIR>
+ <PAIR_PARAMS></PAIR_PARAMS>
+ <POST_RUN_COMMAND></POST_RUN_COMMAND>
+ <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
+ <PURE_BASES>12</PURE_BASES>
+ <QCAL_SOURCE></QCAL_SOURCE>
+ <QCAL_SOURCE1></QCAL_SOURCE1>
+ <QCAL_SOURCE2></QCAL_SOURCE2>
+ <QF_PARAMS>'((CHASTITY>=0.6))'</QF_PARAMS>
+ <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
+ <QTABLE_PATH></QTABLE_PATH>
+ <QTABLE_PATH1></QTABLE_PATH1>
+ <QTABLE_PATH2></QTABLE_PATH2>
+ <QTABLE_REQUIRED>0</QTABLE_REQUIRED>
+ <QTABLE_REQUIRED1>0</QTABLE_REQUIRED1>
+ <QTABLE_REQUIRED2>0</QTABLE_REQUIRED2>
+ <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
+ <READ_LENGTH>37</READ_LENGTH>
+ <READ_LENGTH1>37</READ_LENGTH1>
+ <READ_LENGTH2>0</READ_LENGTH2>
+ <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>
+ <SMT_FILTER>chastity</SMT_FILTER>
+ <SMT_RELATION>ge</SMT_RELATION>
+ <SMT_THRESHOLD>0.6</SMT_THRESHOLD>
+ <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp</SOFTWARE_VERSION>
+ <SRF_2ND_CYCLE></SRF_2ND_CYCLE>
+ <SRF_ARCHIVE_REQUIRED></SRF_ARCHIVE_REQUIRED>
+ <SRF_CHASTITY>0.6</SRF_CHASTITY>
+ <SRF_FILE_SUFFIX>_traces.srf</SRF_FILE_SUFFIX>
+ <SRF_PROCESSED>-P</SRF_PROCESSED>
+ <SRF_QCAL></SRF_QCAL>
+ <SRF_RAW>-R</SRF_RAW>
+ <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
+ <TILE_ROOT>s</TILE_ROOT>
+ <TIME_STAMP>Sun Feb 22 21:15:59 2009</TIME_STAMP>
+ <TOOLS_DIR>/home/diane/proj/GAPipeline-1.0/Goat/../Gerald</TOOLS_DIR>
+ <USE_BASES>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</USE_BASES>
+ <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
+</ChipWideRunParameters>
+<LaneSpecificRunParameters>
+ <ANALYSIS>
+ <s_1>eland_extended</s_1>
+ <s_2>eland_extended</s_2>
+ <s_3>eland_extended</s_3>
+ <s_4>eland_extended</s_4>
+ <s_5>eland_extended</s_5>
+ <s_6>eland_extended</s_6>
+ <s_7>eland_extended</s_7>
+ <s_8>eland_extended</s_8>
+ </ANALYSIS>
+ <ELAND_GENOME>
+ <s_1>/g/mm9</s_1>
+ <s_2>/g/mm9</s_2>
+ <s_3>/g/elegans190</s_3>
+ <s_4>/g/arabidopsis01222004</s_4>
+ <s_5>/g/mm9</s_5>
+ <s_6>/g/mm9</s_6>
+ <s_7>/g/mm9</s_7>
+ <s_8>/g/mm9</s_8>
+ </ELAND_GENOME>
+ <QTABLE_PATH>
+ <s_1>s_1$(QTABLE_SUFFIX)</s_1>
+ <s_2>s_2$(QTABLE_SUFFIX)</s_2>
+ <s_3>s_3$(QTABLE_SUFFIX)</s_3>
+ <s_4>s_4$(QTABLE_SUFFIX)</s_4>
+ <s_5>s_5$(QTABLE_SUFFIX)</s_5>
+ <s_6>s_6$(QTABLE_SUFFIX)</s_6>
+ <s_7>s_7$(QTABLE_SUFFIX)</s_7>
+ <s_8>s_8$(QTABLE_SUFFIX)</s_8>
+ </QTABLE_PATH>
+ <QTABLE_REQUIRED>
+ <s_1>1</s_1>
+ <s_2>1</s_2>
+ <s_3>1</s_3>
+ <s_4>1</s_4>
+ <s_5>1</s_5>
+ <s_6>1</s_6>
+ <s_7>1</s_7>
+ <s_8>1</s_8>
+ </QTABLE_REQUIRED>
+ <READ_LENGTH>
+ <s_1>37</s_1>
+ <s_2>37</s_2>
+ <s_3>37</s_3>
+ <s_4>37</s_4>
+ <s_5>37</s_5>
+ <s_6>37</s_6>
+ <s_7>37</s_7>
+ <s_8>37</s_8>
+ </READ_LENGTH>
+ <SRF_2ND_CYCLE>
+ <s_1></s_1>
+ <s_2></s_2>
+ <s_3></s_3>
+ <s_4></s_4>
+ <s_5></s_5>
+ <s_6></s_6>
+ <s_7></s_7>
+ <s_8></s_8>
+ </SRF_2ND_CYCLE>
+ <SRF_ARCHIVE_REQUIRED>
+ <s_1></s_1>
+ <s_2></s_2>
+ <s_3></s_3>
+ <s_4></s_4>
+ <s_5></s_5>
+ <s_6></s_6>
+ <s_7></s_7>
+ <s_8></s_8>
+ </SRF_ARCHIVE_REQUIRED>
+ <USE_BASES>
+ <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
+ <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
+ <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
+ <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
+ <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
+ <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
+ <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
+ <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
+ </USE_BASES>
+</LaneSpecificRunParameters>
+</RunParameters>
projects / htsworkflow.git / commitdiff