2 Create simulated solexa/illumina runfolders for testing
7 def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
8 firecrest_dir = os.path.join(data_dir,
9 'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
11 os.mkdir(firecrest_dir)
14 def make_ipar_dir(data_dir):
16 Construct an artificial ipar parameter file and directory
18 params = """<?xml version="1.0"?>
20 <Run Name="IPAR_1.01">
21 <Software Name="IPAR" Version="2.01.192.0" />
22 <Cycles First="1" Last="37" Number="37" />
24 <ImagingReads Index="1">
25 <FirstCycle>1</FirstCycle>
26 <LastCycle>37</LastCycle>
27 <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
30 <FirstCycle>1</FirstCycle>
31 <LastCycle>37</LastCycle>
32 <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
34 <Compression>gzip</Compression>
35 <CompressionSuffix>.p.gz</CompressionSuffix>
36 <Instrument>HWI-EAS229</Instrument>
37 <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
40 <AutoOffsetFlag>1</AutoOffsetFlag>
42 <RemappingDistance>1.5</RemappingDistance>
43 <Threshold>4</Threshold>
48 <TileRange Max="100" Min="1" />
52 <TileRange Max="100" Min="1" />
56 <TileRange Max="100" Min="1" />
60 <TileRange Max="100" Min="1" />
64 <TileRange Max="100" Min="1" />
68 <TileRange Max="100" Min="1" />
72 <TileRange Max="100" Min="1" />
76 <TileRange Max="100" Min="1" />
82 f = open(os.path.join(data_dir, '.params'),'w')
85 ipar_dir = os.path.join(data_dir, 'IPAR_1.01')
86 if not os.path.exists(ipar_dir):
90 def make_flowcell_id(runfolder_dir, flowcell_id=None):
91 if flowcell_id is None:
92 flowcell_id = '207BTAAXY'
94 config = """<?xml version="1.0"?>
97 </FlowcellId>""" % (flowcell_id,)
98 config_dir = os.path.join(runfolder_dir, 'Config')
100 if not os.path.exists(config_dir):
102 pathname = os.path.join(config_dir, 'FlowcellId.xml')
103 f = open(pathname,'w')
107 def make_matrix(matrix_dir):
108 contents = """# Auto-generated frequency response matrix
113 0.77 0.15 -0.04 -0.04
114 0.76 1.02 -0.05 -0.06
115 -0.10 -0.10 1.17 -0.03
116 -0.13 -0.12 0.80 1.27
118 s_matrix = os.path.join(matrix_dir, 's_matrix.txt')
119 f = open(s_matrix, 'w')
123 def make_phasing_params(bustard_dir):
124 for lane in range(1,9):
125 pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
126 f = open(pathname, 'w')
127 f.write("""<Parameters>
128 <Phasing>0.009900</Phasing>
129 <Prephasing>0.003500</Prephasing>
134 def make_gerald_config(gerald_dir):
135 config_xml = """<RunParameters>
136 <ChipWideRunParameters>
137 <ANALYSIS>default</ANALYSIS>
138 <BAD_LANES></BAD_LANES>
139 <BAD_TILES></BAD_TILES>
140 <CONTAM_DIR></CONTAM_DIR>
141 <CONTAM_FILE></CONTAM_FILE>
142 <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
143 <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
144 <ELAND_REPEAT></ELAND_REPEAT>
145 <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
146 <EMAIL_LIST>diane</EMAIL_LIST>
147 <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
148 <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>
149 <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
151 <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
152 <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
153 <HAMSTER_FLAG>genome</HAMSTER_FLAG>
154 <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>
155 <POST_RUN_COMMAND></POST_RUN_COMMAND>
156 <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
157 <PURE_BASES>12</PURE_BASES>
158 <QF_PARAMS>'((CHASTITY>=0.6))'</QF_PARAMS>
159 <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
160 <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
161 <READ_LENGTH>32</READ_LENGTH>
162 <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
163 <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
164 <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
165 <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
166 <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
167 <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
168 <TILE_ROOT>s</TILE_ROOT>
169 <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
170 <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
171 <USE_BASES>all</USE_BASES>
172 <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
173 </ChipWideRunParameters>
174 <LaneSpecificRunParameters>
187 <s_2>/g/equcab1</s_2>
188 <s_3>/g/equcab1</s_3>
189 <s_4>/g/canfam2</s_4>
206 <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
207 <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
208 <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
209 <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
210 <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
211 <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
212 <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
213 <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
215 </LaneSpecificRunParameters>
218 pathname = os.path.join(gerald_dir, 'config.xml')
219 f = open(pathname,'w')
223 def make_summary100_htm(gerald_dir):
224 summary_htm="""<!--RUN_TIME Wed Jul 2 06:47:44 2008 -->
225 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
229 <a name="Top"><h2><title>080627_HWI-EAS229_0036_3055HAXX Summary</title></h2></a>
230 <h1>Summary Information For Experiment 080627_HWI-EAS229_0036_3055HAXX on Machine HWI-EAS229</h1>
231 <h2><br></br>Chip Summary<br></br></h2>
232 <table border="1" cellpadding="5">
233 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
234 <tr><td>Run Folder</td><td>080627_HWI-EAS229_0036_3055HAXX</td></tr>
235 <tr><td>Chip ID</td><td>unknown</td></tr>
237 <h2><br></br>Chip Results Summary<br></br></h2>
238 <table border="1" cellpadding="5">
241 <td>Clusters (PF)</td>
242 <td>Yield (kbases)</td>
244 <tr><td>80933224</td>
249 <h2><br></br>Lane Parameter Summary<br></br></h2>
250 <table border="1" cellpadding="5">
254 <td>Sample Target</td>
267 <td>'((CHASTITY>=0.6))'</td>
269 <td><a href="#Lane1">Lane 1</a></td>
277 <td>'((CHASTITY>=0.6))'</td>
279 <td><a href="#Lane2">Lane 2</a></td>
287 <td>'((CHASTITY>=0.6))'</td>
289 <td><a href="#Lane3">Lane 3</a></td>
297 <td>'((CHASTITY>=0.6))'</td>
299 <td><a href="#Lane4">Lane 4</a></td>
307 <td>'((CHASTITY>=0.6))'</td>
309 <td><a href="#Lane5">Lane 5</a></td>
317 <td>'((CHASTITY>=0.6))'</td>
319 <td><a href="#Lane6">Lane 6</a></td>
327 <td>'((CHASTITY>=0.6))'</td>
329 <td><a href="#Lane7">Lane 7</a></td>
337 <td>'((CHASTITY>=0.6))'</td>
339 <td><a href="#Lane8">Lane 8</a></td>
342 <h2><br></br>Lane Results Summary<br></br></h2>
343 <table border="1" cellpadding="5">
345 <td colspan="2">Lane Info</td>
346 <td colspan="8">Tile Mean +/- SD for Lane</td>
350 <td>Lane Yield (kbases) </td>
351 <td>Clusters (raw)</td>
352 <td>Clusters (PF) </td>
353 <td>1st Cycle Int (PF) </td>
354 <td>% intensity after 20 cycles (PF) </td>
355 <td>% PF Clusters </td>
356 <td>% Align (PF) </td>
357 <td>Alignment Score (PF) </td>
358 <td> % Error Rate (PF) </td>
363 <td>96483 +/- 9074</td>
364 <td>60787 +/- 4240</td>
366 <td>101.88 +/- 6.03</td>
367 <td>63.21 +/- 3.29</td>
368 <td>70.33 +/- 0.24</td>
369 <td>9054.08 +/- 59.16</td>
370 <td>0.46 +/- 0.18</td>
375 <td>133738 +/- 7938</td>
376 <td>60217 +/- 1926</td>
378 <td>92.62 +/- 7.58</td>
379 <td>45.20 +/- 3.31</td>
380 <td>51.98 +/- 0.74</td>
381 <td>6692.04 +/- 92.49</td>
382 <td>0.46 +/- 0.09</td>
387 <td>152142 +/- 10002</td>
388 <td>71468 +/- 2827</td>
390 <td>91.53 +/- 8.66</td>
391 <td>47.19 +/- 3.80</td>
392 <td>82.24 +/- 0.44</td>
393 <td>10598.68 +/- 64.13</td>
394 <td>0.41 +/- 0.04</td>
399 <td>15784 +/- 2162</td>
400 <td>13443 +/- 1728</td>
402 <td>97.53 +/- 9.87</td>
403 <td>85.29 +/- 1.91</td>
404 <td>80.02 +/- 0.53</td>
405 <td>10368.82 +/- 71.08</td>
406 <td>0.15 +/- 0.05</td>
411 <td>119735 +/- 8465</td>
412 <td>64590 +/- 2529</td>
414 <td>88.69 +/- 14.79</td>
415 <td>54.10 +/- 2.59</td>
416 <td>76.95 +/- 0.32</td>
417 <td>9936.47 +/- 65.75</td>
418 <td>0.28 +/- 0.02</td>
423 <td>152177 +/- 8146</td>
424 <td>66716 +/- 2493</td>
426 <td>87.06 +/- 9.86</td>
427 <td>43.98 +/- 3.12</td>
428 <td>78.80 +/- 0.43</td>
429 <td>10162.28 +/- 49.65</td>
430 <td>0.38 +/- 0.03</td>
435 <td>84649 +/- 7325</td>
436 <td>57418 +/- 3617</td>
438 <td>89.40 +/- 8.23</td>
439 <td>67.97 +/- 1.82</td>
440 <td>33.38 +/- 0.25</td>
441 <td>4247.92 +/- 32.37</td>
442 <td>1.00 +/- 0.03</td>
447 <td>54622 +/- 4812</td>
448 <td>41136 +/- 3309</td>
450 <td>90.21 +/- 9.10</td>
451 <td>75.39 +/- 2.27</td>
452 <td>48.33 +/- 0.29</td>
453 <td>6169.21 +/- 169.50</td>
454 <td>0.86 +/- 1.22</td>
456 <tr><td colspan="13">Tile mean across chip</td></tr>
470 <h2><br></br>Expanded Lane Summary<br></br></h2>
471 <table border="1" cellpadding="5">
474 <tr><td colspan="2">Lane Info</td>
475 <td colspan="2">Phasing Info</td>
476 <td colspan="2">Raw Data (tile mean)</td>
477 <td colspan="7">Filtered Data (tile mean)</td></tr>
479 <td>Clusters (tile mean) (raw)</td>
481 <td>% Prephasing </td>
482 <td>% Error Rate (raw) </td>
483 <td> Equiv Perfect Clusters (raw) </td>
485 <td>Cycle 2-4 Av Int (PF) </td>
486 <td>Cycle 2-10 Av % Loss (PF) </td>
487 <td>Cycle 10-20 Av % Loss (PF) </td>
488 <td>% Align (PF) </td>
489 <td>% Error Rate (PF) </td>
490 <td> Equiv Perfect Clusters (PF) </td>
501 <td>0.13 +/- 0.44</td>
502 <td>-1.14 +/- 0.34</td>
516 <td>0.29 +/- 0.40</td>
517 <td>-0.79 +/- 0.35</td>
531 <td>0.68 +/- 0.51</td>
532 <td>-0.77 +/- 0.42</td>
546 <td>0.20 +/- 0.69</td>
547 <td>-1.28 +/- 0.66</td>
561 <td>0.34 +/- 0.49</td>
562 <td>-1.55 +/- 4.69</td>
576 <td>0.57 +/- 0.50</td>
577 <td>-0.91 +/- 0.39</td>
591 <td>1.15 +/- 0.52</td>
592 <td>-0.84 +/- 0.58</td>
606 <td>1.10 +/- 0.59</td>
607 <td>-1.01 +/- 0.47</td>
613 <b><br></br>IVC Plots</b>
614 <p> <a href='IVC.htm' target="_blank"> IVC.htm
616 <b><br></br>All Intensity Plots</b>
617 <p> <a href='All.htm' target="_blank"> All.htm
619 <b><br></br>Error graphs: </b>
620 <p> <a href='Error.htm' target="_blank"> Error.htm
622 <td><a href="#Top">Back to top</a></td>
623 <a name="Lane1"><h2><br></br>Lane 1<br></br></h2></a>
624 <table border="1" cellpadding="5">
628 <td>Clusters (raw)</td>
629 <td>Av 1st Cycle Int (PF) </td>
630 <td>Av % intensity after 20 cycles (PF) </td>
631 <td>% PF Clusters </td>
632 <td>% Align (PF) </td>
633 <td>Av Alignment Score (PF) </td>
634 <td>% Error Rate (PF) </td>
648 <td><a href="#Top">Back to top</a></td>
649 <a name="Lane2"><h2><br></br>Lane 2<br></br></h2></a>
650 <table border="1" cellpadding="5">
654 <td>Clusters (raw)</td>
655 <td>Av 1st Cycle Int (PF) </td>
656 <td>Av % intensity after 20 cycles (PF) </td>
657 <td>% PF Clusters </td>
658 <td>% Align (PF) </td>
659 <td>Av Alignment Score (PF) </td>
660 <td>% Error Rate (PF) </td>
674 <td><a href="#Top">Back to top</a></td>
675 <a name="Lane3"><h2><br></br>Lane 3<br></br></h2></a>
676 <table border="1" cellpadding="5">
680 <td>Clusters (raw)</td>
681 <td>Av 1st Cycle Int (PF) </td>
682 <td>Av % intensity after 20 cycles (PF) </td>
683 <td>% PF Clusters </td>
684 <td>% Align (PF) </td>
685 <td>Av Alignment Score (PF) </td>
686 <td>% Error Rate (PF) </td>
700 <td><a href="#Top">Back to top</a></td>
701 <a name="Lane4"><h2><br></br>Lane 4<br></br></h2></a>
702 <table border="1" cellpadding="5">
706 <td>Clusters (raw)</td>
707 <td>Av 1st Cycle Int (PF) </td>
708 <td>Av % intensity after 20 cycles (PF) </td>
709 <td>% PF Clusters </td>
710 <td>% Align (PF) </td>
711 <td>Av Alignment Score (PF) </td>
712 <td>% Error Rate (PF) </td>
726 <td><a href="#Top">Back to top</a></td>
727 <a name="Lane5"><h2><br></br>Lane 5<br></br></h2></a>
728 <table border="1" cellpadding="5">
732 <td>Clusters (raw)</td>
733 <td>Av 1st Cycle Int (PF) </td>
734 <td>Av % intensity after 20 cycles (PF) </td>
735 <td>% PF Clusters </td>
736 <td>% Align (PF) </td>
737 <td>Av Alignment Score (PF) </td>
738 <td>% Error Rate (PF) </td>
741 <td><a href="#Top">Back to top</a></td>
742 <a name="Lane6"><h2><br></br>Lane 6<br></br></h2></a>
743 <table border="1" cellpadding="5">
747 <td>Clusters (raw)</td>
748 <td>Av 1st Cycle Int (PF) </td>
749 <td>Av % intensity after 20 cycles (PF) </td>
750 <td>% PF Clusters </td>
751 <td>% Align (PF) </td>
752 <td>Av Alignment Score (PF) </td>
753 <td>% Error Rate (PF) </td>
767 <td><a href="#Top">Back to top</a></td>
768 <a name="Lane7"><h2><br></br>Lane 7<br></br></h2></a>
769 <table border="1" cellpadding="5">
773 <td>Clusters (raw)</td>
774 <td>Av 1st Cycle Int (PF) </td>
775 <td>Av % intensity after 20 cycles (PF) </td>
776 <td>% PF Clusters </td>
777 <td>% Align (PF) </td>
778 <td>Av Alignment Score (PF) </td>
779 <td>% Error Rate (PF) </td>
793 <td><a href="#Top">Back to top</a></td>
794 <a name="Lane8"><h2><br></br>Lane 8<br></br></h2></a>
795 <table border="1" cellpadding="5">
799 <td>Clusters (raw)</td>
800 <td>Av 1st Cycle Int (PF) </td>
801 <td>Av % intensity after 20 cycles (PF) </td>
802 <td>% PF Clusters </td>
803 <td>% Align (PF) </td>
804 <td>Av Alignment Score (PF) </td>
805 <td>% Error Rate (PF) </td>
819 <td><a href="#Top">Back to top</a></td>
823 pathname = os.path.join(gerald_dir, 'Summary.htm')
824 f = open(pathname, 'w')
828 def make_summary_paired_htm(gerald_dir):
829 summary_htm = """<!--RUN_TIME Thu Nov 13 15:11:29 2008 -->
830 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
834 <a name="Top"><h2><title>080920_HWI-EAS229_0057_30GBJAAXX Summary</title></h2></a>
835 <h1>Summary Information For Experiment 080920_HWI-EAS229_0057_30GBJAAXX on Machine unknown</h1>
836 <h2><br></br>Chip Summary<br></br></h2>
837 <table border="1" cellpadding="5">
838 <tr><td>Machine</td><td>UNKNOWN</td></tr>
839 <tr><td>Run Folder</td><td>080920_HWI-EAS229_0057_30GBJAAXX</td></tr>
840 <tr><td>Chip ID</td><td>unknown</td></tr>
842 <h2><br></br>Chip Results Summary<br></br></h2>
843 <table border="1" cellpadding="5">
846 <td>Clusters (PF)</td>
847 <td>Yield (kbases)</td>
849 <tr><td>126151880</td>
854 <h2><br></br>Lane Parameter Summary<br></br></h2>
855 <table border="1" cellpadding="5">
859 <td>Sample Target</td>
872 <td>'((CHASTITY>=0.6))'</td>
874 <td><a href="#Lane1">Lane 1</a></td>
882 <td>'((CHASTITY>=0.6))'</td>
884 <td><a href="#Lane2">Lane 2</a></td>
892 <td>'((CHASTITY>=0.6))'</td>
894 <td><a href="#Lane3">Lane 3</a></td>
902 <td>'((CHASTITY>=0.6))'</td>
904 <td><a href="#Lane4">Lane 4</a></td>
912 <td>'((CHASTITY>=0.6))'</td>
914 <td><a href="#Lane5">Lane 5</a></td>
922 <td>'((CHASTITY>=0.6))'</td>
924 <td><a href="#Lane6">Lane 6</a></td>
932 <td>'((CHASTITY>=0.6))'</td>
934 <td><a href="#Lane7">Lane 7</a></td>
942 <td>'((CHASTITY>=0.6))'</td>
944 <td><a href="#Lane8">Lane 8</a></td>
947 <h2><br></br>Lane Results Summary : Read 1<br></br></h2>
948 <table border="1" cellpadding="5">
950 <td colspan="2">Lane Info</td>
951 <td colspan="8">Tile Mean +/- SD for Lane</td>
955 <td>Lane Yield (kbases) </td>
956 <td>Clusters (raw)</td>
957 <td>Clusters (PF) </td>
958 <td>1st Cycle Int (PF) </td>
959 <td>% intensity after 20 cycles (PF) </td>
960 <td>% PF Clusters </td>
961 <td>% Align (PF) </td>
962 <td>Alignment Score (PF) </td>
963 <td> % Error Rate (PF) </td>
968 <td>103646 +/- 4515</td>
969 <td>74887 +/- 6080</td>
971 <td>99.34 +/- 3.52</td>
972 <td>72.22 +/- 4.63</td>
973 <td>89.19 +/- 0.59</td>
974 <td>14.16 +/- 0.63</td>
975 <td>0.94 +/- 0.17</td>
980 <td>106678 +/- 4652</td>
981 <td>78260 +/- 2539</td>
983 <td>98.23 +/- 2.66</td>
984 <td>73.43 +/- 2.52</td>
985 <td>87.05 +/- 0.64</td>
986 <td>16.81 +/- 0.55</td>
987 <td>0.92 +/- 0.17</td>
992 <td>84583 +/- 5963</td>
993 <td>70065 +/- 4194</td>
995 <td>99.82 +/- 3.05</td>
996 <td>82.90 +/- 1.32</td>
997 <td>89.49 +/- 0.20</td>
998 <td>18.13 +/- 0.66</td>
999 <td>0.81 +/- 0.13</td>
1004 <td>68813 +/- 4782</td>
1005 <td>56905 +/- 4145</td>
1007 <td>102.00 +/- 14.74</td>
1008 <td>82.91 +/- 5.89</td>
1009 <td>56.93 +/- 0.82</td>
1010 <td>25.85 +/- 2.30</td>
1011 <td>0.95 +/- 0.30</td>
1016 <td>104854 +/- 4664</td>
1017 <td>79879 +/- 6270</td>
1019 <td>98.26 +/- 5.85</td>
1020 <td>76.34 +/- 6.67</td>
1021 <td>57.71 +/- 0.30</td>
1022 <td>26.16 +/- 1.68</td>
1023 <td>0.97 +/- 0.19</td>
1028 <td>43555 +/- 1632</td>
1029 <td>37946 +/- 2140</td>
1031 <td>105.74 +/- 8.40</td>
1032 <td>87.14 +/- 3.87</td>
1033 <td>89.08 +/- 1.00</td>
1034 <td>33.53 +/- 2.18</td>
1035 <td>1.05 +/- 0.21</td>
1040 <td>54265 +/- 1588</td>
1041 <td>41680 +/- 5319</td>
1043 <td>111.33 +/- 8.90</td>
1044 <td>76.94 +/- 10.52</td>
1045 <td>84.50 +/- 1.41</td>
1046 <td>27.44 +/- 2.33</td>
1047 <td>1.32 +/- 0.25</td>
1052 <td>64363 +/- 2697</td>
1053 <td>39991 +/- 6785</td>
1055 <td>109.93 +/- 7.80</td>
1056 <td>62.45 +/- 12.05</td>
1057 <td>82.20 +/- 2.08</td>
1058 <td>24.63 +/- 2.53</td>
1059 <td>1.57 +/- 0.22</td>
1061 <tr><td colspan="13">Tile mean across chip</td></tr>
1075 <h2><br></br>Lane Results Summary : Read 2<br></br></h2>
1076 <table border="1" cellpadding="5">
1078 <td colspan="2">Lane Info</td>
1079 <td colspan="8">Tile Mean +/- SD for Lane</td>
1083 <td>Lane Yield (kbases) </td>
1084 <td>Clusters (raw)</td>
1085 <td>Clusters (PF) </td>
1086 <td>1st Cycle Int (PF) </td>
1087 <td>% intensity after 20 cycles (PF) </td>
1088 <td>% PF Clusters </td>
1089 <td>% Align (PF) </td>
1090 <td>Alignment Score (PF) </td>
1091 <td> % Error Rate (PF) </td>
1096 <td>103646 +/- 4515</td>
1097 <td>74887 +/- 6080</td>
1099 <td>94.42 +/- 5.68</td>
1100 <td>72.22 +/- 4.63</td>
1101 <td>81.54 +/- 2.13</td>
1102 <td>42.70 +/- 5.49</td>
1103 <td>0.89 +/- 0.27</td>
1108 <td>106678 +/- 4652</td>
1109 <td>78260 +/- 2539</td>
1111 <td>93.57 +/- 2.55</td>
1112 <td>73.43 +/- 2.52</td>
1113 <td>82.05 +/- 0.37</td>
1114 <td>43.98 +/- 3.02</td>
1115 <td>0.76 +/- 0.15</td>
1120 <td>84583 +/- 5963</td>
1121 <td>70065 +/- 4194</td>
1123 <td>94.23 +/- 2.19</td>
1124 <td>82.90 +/- 1.32</td>
1125 <td>84.94 +/- 0.28</td>
1126 <td>51.76 +/- 2.29</td>
1127 <td>0.59 +/- 0.07</td>
1132 <td>68813 +/- 4782</td>
1133 <td>56905 +/- 4145</td>
1135 <td>96.82 +/- 7.12</td>
1136 <td>82.91 +/- 5.89</td>
1137 <td>56.01 +/- 0.99</td>
1138 <td>27.86 +/- 3.48</td>
1139 <td>0.95 +/- 0.33</td>
1144 <td>104854 +/- 4664</td>
1145 <td>79879 +/- 6270</td>
1147 <td>103.56 +/- 15.45</td>
1148 <td>76.34 +/- 6.67</td>
1149 <td>56.76 +/- 0.41</td>
1150 <td>25.68 +/- 2.06</td>
1151 <td>0.98 +/- 0.17</td>
1156 <td>43555 +/- 1632</td>
1157 <td>37946 +/- 2140</td>
1159 <td>100.82 +/- 5.47</td>
1160 <td>87.14 +/- 3.87</td>
1161 <td>88.64 +/- 1.42</td>
1162 <td>34.05 +/- 2.60</td>
1163 <td>0.98 +/- 0.22</td>
1168 <td>54265 +/- 1588</td>
1169 <td>41680 +/- 5319</td>
1171 <td>103.42 +/- 3.47</td>
1172 <td>76.94 +/- 10.52</td>
1173 <td>83.90 +/- 1.32</td>
1174 <td>27.60 +/- 2.07</td>
1175 <td>1.26 +/- 0.16</td>
1180 <td>64363 +/- 2697</td>
1181 <td>39991 +/- 6785</td>
1183 <td>99.48 +/- 3.23</td>
1184 <td>62.45 +/- 12.05</td>
1185 <td>79.81 +/- 3.35</td>
1186 <td>23.06 +/- 2.50</td>
1187 <td>1.56 +/- 0.23</td>
1189 <tr><td colspan="13">Tile mean across chip</td></tr>
1203 <h2><br></br>Expanded Lane Summary : Read 1<br></br></h2>
1204 <table border="1" cellpadding="5">
1207 <tr><td colspan="2">Lane Info</td>
1208 <td colspan="2">Phasing Info</td>
1209 <td colspan="2">Raw Data (tile mean)</td>
1210 <td colspan="7">Filtered Data (tile mean)</td></tr>
1212 <td>Clusters (tile mean) (raw)</td>
1214 <td>% Prephasing </td>
1215 <td>% Error Rate (raw) </td>
1216 <td> Equiv Perfect Clusters (raw) </td>
1217 <td>% retained </td>
1218 <td>Cycle 2-4 Av Int (PF) </td>
1219 <td>Cycle 2-10 Av % Loss (PF) </td>
1220 <td>Cycle 10-20 Av % Loss (PF) </td>
1221 <td>% Align (PF) </td>
1222 <td>% Error Rate (PF) </td>
1223 <td> Equiv Perfect Clusters (PF) </td>
1234 <td>-0.53 +/- 0.37</td>
1235 <td>-0.42 +/- 0.21</td>
1249 <td>0.08 +/- 0.43</td>
1250 <td>-0.17 +/- 0.34</td>
1264 <td>0.29 +/- 0.48</td>
1265 <td>-0.02 +/- 0.17</td>
1279 <td>-0.01 +/- 0.62</td>
1280 <td>-0.37 +/- 0.30</td>
1294 <td>-0.03 +/- 0.46</td>
1295 <td>-0.49 +/- 0.27</td>
1309 <td>-0.19 +/- 0.46</td>
1310 <td>-0.34 +/- 0.40</td>
1324 <td>-0.41 +/- 0.49</td>
1325 <td>-0.55 +/- 0.23</td>
1339 <td>-0.52 +/- 0.36</td>
1340 <td>-0.29 +/- 0.19</td>
1346 <h2><br></br>Expanded Lane Summary : Read 2<br></br></h2>
1347 <table border="1" cellpadding="5">
1350 <tr><td colspan="2">Lane Info</td>
1351 <td colspan="2">Phasing Info</td>
1352 <td colspan="2">Raw Data (tile mean)</td>
1353 <td colspan="7">Filtered Data (tile mean)</td></tr>
1355 <td>Clusters (tile mean) (raw)</td>
1357 <td>% Prephasing </td>
1358 <td>% Error Rate (raw) </td>
1359 <td> Equiv Perfect Clusters (raw) </td>
1360 <td>% retained </td>
1361 <td>Cycle 2-4 Av Int (PF) </td>
1362 <td>Cycle 2-10 Av % Loss (PF) </td>
1363 <td>Cycle 10-20 Av % Loss (PF) </td>
1364 <td>% Align (PF) </td>
1365 <td>% Error Rate (PF) </td>
1366 <td> Equiv Perfect Clusters (PF) </td>
1377 <td>-0.53 +/- 0.37</td>
1378 <td>-0.42 +/- 0.21</td>
1392 <td>0.08 +/- 0.43</td>
1393 <td>-0.17 +/- 0.34</td>
1407 <td>0.29 +/- 0.48</td>
1408 <td>-0.02 +/- 0.17</td>
1422 <td>-0.01 +/- 0.62</td>
1423 <td>-0.37 +/- 0.30</td>
1437 <td>-0.03 +/- 0.46</td>
1438 <td>-0.49 +/- 0.27</td>
1452 <td>-0.19 +/- 0.46</td>
1453 <td>-0.34 +/- 0.40</td>
1467 <td>-0.41 +/- 0.49</td>
1468 <td>-0.55 +/- 0.23</td>
1482 <td>-0.52 +/- 0.36</td>
1483 <td>-0.29 +/- 0.19</td>
1491 pathname = os.path.join(gerald_dir, 'Summary.htm')
1492 f = open(pathname, 'w')
1493 f.write(summary_htm)
1496 def make_eland_results(gerald_dir):
1497 eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
1498 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T
1499 >HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
1500 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
1502 for i in range(1,9):
1503 pathname = os.path.join(gerald_dir,
1504 's_%d_eland_result.txt' % (i,))
1505 f = open(pathname, 'w')
1506 f.write(eland_result)
1509 def make_eland_multi(gerald_dir):
1510 eland_multi = """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
1511 >HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
1512 >HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
1513 >HWI-EAS229_60_30DP9AAXX:1:1:892:1155 ACATTCTCCTTTCCTTCTGAAGTTTTTACGATTCTTT 0:9:10 chr10.fa:114298201F1,chr12.fa:8125072F1,19500297F2,42341293R2,chr13.fa:27688155R2,95069772R1,chr15.fa:51016475F2,chr16.fa:27052155F2,chr1.fa:192426217R2,chr21.fa:23685310R2,chr2.fa:106680068F1,chr3.fa:185226695F2,chr4.fa:106626808R2,chr5.fa:14704894F1,43530779F1,126543189F2,chr6.fa:74284101F1,chr7.fa:22516603F1,chr9.fa:134886204R
1515 for i in range(1,9):
1516 pathname = os.path.join(gerald_dir,
1517 's_%d_eland_multi.txt' % (i,))
1518 f = open(pathname, 'w')
1519 f.write(eland_multi)