f.write(summary_htm)
f.close()
+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()
+
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 $-->
--- /dev/null
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+import unittest
+
+from htsworkflow.pipelines import firecrest
+from htsworkflow.pipelines import bustard
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.runfolder import ElementTree
+
+from htsworkflow.pipelines.test.simulate_runfolder import *
+
+
+def make_runfolder(obj=None):
+ """
+ Make a fake runfolder, attach all the directories to obj if defined
+ """
+ # make a fake runfolder directory
+ temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
+
+ runfolder_dir = os.path.join(temp_dir,
+ '081017_HWI-EAS229_0062_30J55AAXX')
+ os.mkdir(runfolder_dir)
+
+ data_dir = os.path.join(runfolder_dir, 'Data')
+ os.mkdir(data_dir)
+
+ firecrest_dir = os.path.join(data_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)
+
+ gerald_dir = os.path.join(bustard_dir,
+ 'GERALD_20-10-2008_diane')
+ os.mkdir(gerald_dir)
+ make_gerald_config(gerald_dir)
+ make_summary_htm_110(gerald_dir)
+ make_eland_multi(gerald_dir)
+
+ if obj is not None:
+ obj.temp_dir = temp_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
+
+
+class RunfolderTests(unittest.TestCase):
+ """
+ Test components of the runfolder processing code
+ which includes firecrest, bustard, and gerald
+ """
+ def setUp(self):
+ # attaches all the directories to the object passed in
+ make_runfolder(self)
+
+ def tearDown(self):
+ shutil.rmtree(self.temp_dir)
+
+ def test_firecrest(self):
+ """
+ Construct a firecrest object
+ """
+ f = firecrest.firecrest(self.image_analysis_dir)
+ self.failUnlessEqual(f.version, '1.9.6')
+ self.failUnlessEqual(f.start, 1)
+ self.failUnlessEqual(f.stop, 37)
+ self.failUnlessEqual(f.user, 'diane')
+ self.failUnlessEqual(f.date, date(2008,10,20))
+
+ xml = f.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+
+ f2 = firecrest.Firecrest(xml=xml)
+ self.failUnlessEqual(f.version, f2.version)
+ self.failUnlessEqual(f.start, f2.start)
+ self.failUnlessEqual(f.stop, f2.stop)
+ self.failUnlessEqual(f.user, f2.user)
+
+ def test_bustard(self):
+ """
+ construct a bustard object
+ """
+ b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.version, '1.9.6')
+ self.failUnlessEqual(b.date, date(2008,10,20))
+ self.failUnlessEqual(b.user, 'diane')
+ self.failUnlessEqual(len(b.phasing), 8)
+ self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
+
+ xml = b.get_elements()
+ b2 = bustard.Bustard(xml=xml)
+ self.failUnlessEqual(b.version, b2.version)
+ self.failUnlessEqual(b.date, b2.date )
+ self.failUnlessEqual(b.user, b2.user)
+ self.failUnlessEqual(len(b.phasing), len(b2.phasing))
+ for key in b.phasing.keys():
+ self.failUnlessEqual(b.phasing[key].lane,
+ b2.phasing[key].lane)
+ self.failUnlessEqual(b.phasing[key].phasing,
+ b2.phasing[key].phasing)
+ self.failUnlessEqual(b.phasing[key].prephasing,
+ b2.phasing[key].prephasing)
+
+ def test_gerald(self):
+ # need to update gerald and make tests for it
+ 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))
+ self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
+ self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
+
+
+ # list of genomes, matches what was defined up in
+ # 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', ]
+
+ # test lane specific parameters from gerald config file
+ for i in range(1,9):
+ cur_lane = g.lanes[str(i)]
+ self.failUnlessEqual(cur_lane.analysis, 'eland')
+ self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
+ self.failUnlessEqual(cur_lane.read_length, '32')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
+
+ # 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)
+
+ # raw cluster numbers extracted from summary file
+ # its the first +/- value in the lane results summary
+ # section
+ clusters = [None,
+ (190220, 15118), (190560, 14399),
+ (187597, 12369), (204142, 16877),
+ (247308, 11600), (204298, 15640),
+ (202707, 15404), (198075, 14702),]
+
+ for i in range(1,9):
+ summary_lane = g.summary[str(i)]
+ self.failUnlessEqual(summary_lane.cluster, clusters[i])
+ self.failUnlessEqual(summary_lane.lane, str(i))
+
+ xml = g.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+ g2 = gerald.Gerald(xml=xml)
+
+ # do it all again after extracting from the xml file
+ self.failUnlessEqual(g.version, g2.version)
+ self.failUnlessEqual(g.date, g2.date)
+ self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
+ self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
+
+ # test lane specific parameters from gerald config file
+ for i in range(1,9):
+ g_lane = g.lanes[str(i)]
+ g2_lane = g2.lanes[str(i)]
+ self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
+ self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
+ self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
+ self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
+
+ # test (some) summary elements
+ for i in range(1,9):
+ g_summary = g.summary[str(i)]
+ g2_summary = g2.summary[str(i)]
+ self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
+ self.failUnlessEqual(g_summary.lane, g2_summary.lane)
+
+ g_eland = g.eland_results
+ g2_eland = g2.eland_results
+ for lane in g_eland.keys():
+ self.failUnlessEqual(g_eland[lane].reads,
+ g2_eland[lane].reads)
+ self.failUnlessEqual(len(g_eland[lane].mapped_reads),
+ len(g2_eland[lane].mapped_reads))
+ for k in g_eland[lane].mapped_reads.keys():
+ self.failUnlessEqual(g_eland[lane].mapped_reads[k],
+ g2_eland[lane].mapped_reads[k])
+
+ self.failUnlessEqual(len(g_eland[lane].match_codes),
+ len(g2_eland[lane].match_codes))
+ for k in g_eland[lane].match_codes.keys():
+ self.failUnlessEqual(g_eland[lane].match_codes[k],
+ g2_eland[lane].match_codes[k])
+
+
+ def test_eland(self):
+ hg_map = {'Lambda.fa': 'Lambda.fa'}
+ for i in range(1,22):
+ short_name = 'chr%d.fa' % (i,)
+ long_name = 'hg18/chr%d.fa' % (i,)
+ hg_map[short_name] = long_name
+
+ genome_maps = { '1':hg_map, '2':hg_map, '3':hg_map, '4':hg_map,
+ '5':hg_map, '6':hg_map, '7':hg_map, '8':hg_map }
+ eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
+
+ for i in range(1,9):
+ lane = eland[str(i)]
+ self.failUnlessEqual(lane.reads, 4)
+ self.failUnlessEqual(lane.sample_name, "s")
+ self.failUnlessEqual(lane.lane_id, unicode(i))
+ self.failUnlessEqual(len(lane.mapped_reads), 15)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+ self.failUnlessEqual(lane.match_codes['U0'], 1)
+ self.failUnlessEqual(lane.match_codes['R0'], 2)
+ self.failUnlessEqual(lane.match_codes['U1'], 1)
+ self.failUnlessEqual(lane.match_codes['R1'], 9)
+ self.failUnlessEqual(lane.match_codes['U2'], 0)
+ self.failUnlessEqual(lane.match_codes['R2'], 12)
+ self.failUnlessEqual(lane.match_codes['NM'], 1)
+ self.failUnlessEqual(lane.match_codes['QC'], 0)
+
+ xml = eland.get_elements()
+ # just make sure that element tree can serialize the tree
+ xml_str = ElementTree.tostring(xml)
+ e2 = gerald.ELAND(xml=xml)
+
+ for i in range(1,9):
+ l1 = eland[str(i)]
+ l2 = e2[str(i)]
+ self.failUnlessEqual(l1.reads, l2.reads)
+ self.failUnlessEqual(l1.sample_name, l2.sample_name)
+ self.failUnlessEqual(l1.lane_id, l2.lane_id)
+ self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
+ self.failUnlessEqual(len(l1.mapped_reads), 15)
+ for k in l1.mapped_reads.keys():
+ self.failUnlessEqual(l1.mapped_reads[k],
+ l2.mapped_reads[k])
+
+ self.failUnlessEqual(len(l1.match_codes), 9)
+ self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
+ for k in l1.match_codes.keys():
+ self.failUnlessEqual(l1.match_codes[k],
+ l2.match_codes[k])
+
+ def test_runfolder(self):
+ runs = runfolder.get_runs(self.runfolder_dir)
+
+ # do we get the flowcell id from the filename?
+ self.failUnlessEqual(len(runs), 1)
+ name = 'run_30J55AAXX_2008-10-20.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'
+ self.failUnlessEqual(runs[0].name, name)
+
+ r1 = runs[0]
+ xml = r1.get_elements()
+ xml_str = ElementTree.tostring(xml)
+
+ r2 = runfolder.PipelineRun(xml=xml)
+ self.failUnlessEqual(r1.name, r2.name)
+ self.failIfEqual(r2.image_analysis, None)
+ self.failIfEqual(r2.bustard, None)
+ self.failIfEqual(r2.gerald, None)
+
+
+def suite():
+ return unittest.makeSuite(RunfolderTests,'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest="suite")
+
projects / htsworkflow.git / commitdiff