"""
import os
+import shutil
+TEST_CODE_DIR = os.path.split(__file__)[0]
+TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
+LANE_LIST = range(1,9)
-def make_ipar_dir(data_dir):
+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)
+ )
+ os.mkdir(firecrest_dir)
+ return firecrest_dir
+
+def make_ipar_dir(data_dir, version='1.01'):
"""
Construct an artificial ipar parameter file and directory
"""
- params = """<?xml version="1.0"?>
-<ImageAnalysis>
- <Run Name="IPAR_1.01">
- <Software Name="IPAR" Version="2.01.192.0" />
- <Cycles First="1" Last="37" Number="37" />
- <RunParameters>
- <ImagingReads Index="1">
- <FirstCycle>1</FirstCycle>
- <LastCycle>37</LastCycle>
- <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
- </ImagingReads>
- <Reads Index="1">
- <FirstCycle>1</FirstCycle>
- <LastCycle>37</LastCycle>
- <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
- </Reads>
- <Compression>gzip</Compression>
- <CompressionSuffix>.p.gz</CompressionSuffix>
- <Instrument>HWI-EAS229</Instrument>
- <RunFolder>081021_HWI-EAS229_0063_30HKUAAXX</RunFolder>
- </RunParameters>
- <ImageParameters>
- <AutoOffsetFlag>1</AutoOffsetFlag>
- <Fwhm>2.7</Fwhm>
- <RemappingDistance>1.5</RemappingDistance>
- <Threshold>4</Threshold>
- </ImageParameters>
- <TileSelection>
- <Lane Index="1">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="2">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="3">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="4">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="5">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="6">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="7">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- <Lane Index="8">
- <Sample>s</Sample>
- <TileRange Max="100" Min="1" />
- </Lane>
- </TileSelection>
- </Run>
-</ImageAnalysis>
-"""
- f = open(os.path.join(data_dir, '.params'),'w')
- f.write(params)
- f.close()
- ipar_dir = os.path.join(data_dir, 'IPAR_1.01')
+ 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_%s' % (version,))
if not os.path.exists(ipar_dir):
os.mkdir(ipar_dir)
return ipar_dir
f.write(config)
f.close()
-def make_matrix(matrix_dir):
+def make_bustard_config132(gerald_dir):
+ source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
+ destination = os.path.join(gerald_dir, 'config.xml')
+ shutil.copy(source, destination)
+
+def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ intensities_dir = os.path.join(data_dir, 'Intensities')
+ if not os.path.exists(intensities_dir):
+ os.mkdir(intensities_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
+ shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
+
+ return intensities_dir
+
+def make_rta_basecalls_1460(intensities_dir):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
+ if not os.path.exists(basecalls_dir):
+ os.mkdir(basecalls_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
+ shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
+
+ return basecalls_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_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)
-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_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)
-<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_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)
-<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_110(gerald_dir):
+ 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):
+ 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):
+ 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.
f = open(pathname, 'w')
f.write(eland_result)
f.close()
+
+def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
+ eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
+>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
+>HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
+>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
+>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
+>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
+""", """>HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
+>HWI-EAS229_60_30DP9AAXX:1:1:1221:788 NNNNNNNNNNNNNNGTGGTATGGCGGTGTCTGGTCGT QC
+>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
+>HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0,chr7.fa:22516603F1,chr9.fa:134886204R
+>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
+>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample1:55269838R0
+>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:0 spike.fa/sample2:55269838R0
+"""]
+ if paired:
+ for e in [1,2]:
+ for i in lane_list:
+ pathname = os.path.join(gerald_dir,
+ 's_%d_%d_eland_multi.txt' % (i,e))
+ f = open(pathname, 'w')
+ f.write(eland_multi[e-1])
+ f.close()
+ else:
+ for i in lane_list:
+ pathname = os.path.join(gerald_dir,
+ 's_%d_eland_multi.txt' % (i,))
+ f = open(pathname, 'w')
+ f.write(eland_multi[0])
+ f.close()
+
+def make_scarf(gerald_dir, lane_list=LANE_LIST):
+ seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
+HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
+HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
+HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
+HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
+"""
+ for l in lane_list:
+ pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
+ f = open(pathname,'w')
+ f.write(seq)
+ f.close()
+
+def make_fastq(gerald_dir, lane_list=LANE_LIST):
+ seq = """@HWI-EAS229:1:2:182:712#0/1
+AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
++HWI-EAS229:1:2:182:712#0/1
+\bab_bbaabbababbaaa]]D]bb_baabbab\baa
+@HWI-EAS229:1:2:198:621#0/1
+CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
++HWI-EAS229:1:2:198:621#0/1
+[aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
+@HWI-EAS229:1:2:209:1321#0/1
+AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
++HWI-EAS229:1:2:209:1321#0/1
+_bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
+"""
+ for l in lane_list:
+ pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
+ f = open(pathname,'w')
+ f.write(seq)
+ f.close()
+
+
projects / htsworkflow.git / blobdiff