3 from datetime import datetime, date
9 from gaworkflow.pipeline import firecrest
10 from gaworkflow.pipeline import bustard
11 from gaworkflow.pipeline import gerald
12 from gaworkflow.pipeline import runfolder
13 from gaworkflow.pipeline.runfolder import ElementTree
16 def make_flowcell_id(runfolder_dir, flowcell_id=None):
17 if flowcell_id is None:
18 flowcell_id = '207BTAAXY'
20 config = """<?xml version="1.0"?>
23 </FlowcellId>""" % (flowcell_id,)
24 config_dir = os.path.join(runfolder_dir, 'Config')
26 if not os.path.exists(config_dir):
28 pathname = os.path.join(config_dir, 'FlowcellId.xml')
29 f = open(pathname,'w')
33 def make_matrix(matrix_dir):
34 contents = """# Auto-generated frequency response matrix
41 -0.10 -0.10 1.17 -0.03
44 s_matrix = os.path.join(matrix_dir, 's_matrix.txt')
45 f = open(s_matrix, 'w')
49 def make_phasing_params(bustard_dir):
50 for lane in range(1,9):
51 pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
52 f = open(pathname, 'w')
53 f.write("""<Parameters>
54 <Phasing>0.009900</Phasing>
55 <Prephasing>0.003500</Prephasing>
60 def make_gerald_config(gerald_dir):
61 config_xml = """<RunParameters>
62 <ChipWideRunParameters>
63 <ANALYSIS>default</ANALYSIS>
64 <BAD_LANES></BAD_LANES>
65 <BAD_TILES></BAD_TILES>
66 <CONTAM_DIR></CONTAM_DIR>
67 <CONTAM_FILE></CONTAM_FILE>
68 <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
69 <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
70 <ELAND_REPEAT></ELAND_REPEAT>
71 <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
72 <EMAIL_LIST>diane</EMAIL_LIST>
73 <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
74 <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>
75 <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
77 <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
78 <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
79 <HAMSTER_FLAG>genome</HAMSTER_FLAG>
80 <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>
81 <POST_RUN_COMMAND></POST_RUN_COMMAND>
82 <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
83 <PURE_BASES>12</PURE_BASES>
84 <QF_PARAMS>'((CHASTITY>=0.6))'</QF_PARAMS>
85 <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
86 <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
87 <READ_LENGTH>32</READ_LENGTH>
88 <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
89 <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
90 <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
91 <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
92 <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
93 <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
94 <TILE_ROOT>s</TILE_ROOT>
95 <TIME_STAMP>Sat Apr 19 19:08:30 2008</TIME_STAMP>
96 <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
97 <USE_BASES>all</USE_BASES>
98 <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
99 </ChipWideRunParameters>
100 <LaneSpecificRunParameters>
113 <s_2>/g/equcab1</s_2>
114 <s_3>/g/equcab1</s_3>
115 <s_4>/g/canfam2</s_4>
132 <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
133 <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
134 <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
135 <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
136 <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
137 <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
138 <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
139 <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
141 </LaneSpecificRunParameters>
144 pathname = os.path.join(gerald_dir, 'config.xml')
145 f = open(pathname,'w')
149 def make_summary_htm(gerald_dir):
150 summary_htm="""<!--RUN_TIME Wed Jul 2 06:47:44 2008 -->
151 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
155 <a name="Top"><h2><title>080627_HWI-EAS229_0036_3055HAXX Summary</title></h2></a>
156 <h1>Summary Information For Experiment 080627_HWI-EAS229_0036_3055HAXX on Machine HWI-EAS229</h1>
157 <h2><br></br>Chip Summary<br></br></h2>
158 <table border="1" cellpadding="5">
159 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
160 <tr><td>Run Folder</td><td>080627_HWI-EAS229_0036_3055HAXX</td></tr>
161 <tr><td>Chip ID</td><td>unknown</td></tr>
163 <h2><br></br>Chip Results Summary<br></br></h2>
164 <table border="1" cellpadding="5">
167 <td>Clusters (PF)</td>
168 <td>Yield (kbases)</td>
170 <tr><td>80933224</td>
175 <h2><br></br>Lane Parameter Summary<br></br></h2>
176 <table border="1" cellpadding="5">
180 <td>Sample Target</td>
193 <td>'((CHASTITY>=0.6))'</td>
195 <td><a href="#Lane1">Lane 1</a></td>
203 <td>'((CHASTITY>=0.6))'</td>
205 <td><a href="#Lane2">Lane 2</a></td>
213 <td>'((CHASTITY>=0.6))'</td>
215 <td><a href="#Lane3">Lane 3</a></td>
223 <td>'((CHASTITY>=0.6))'</td>
225 <td><a href="#Lane4">Lane 4</a></td>
233 <td>'((CHASTITY>=0.6))'</td>
235 <td><a href="#Lane5">Lane 5</a></td>
243 <td>'((CHASTITY>=0.6))'</td>
245 <td><a href="#Lane6">Lane 6</a></td>
253 <td>'((CHASTITY>=0.6))'</td>
255 <td><a href="#Lane7">Lane 7</a></td>
263 <td>'((CHASTITY>=0.6))'</td>
265 <td><a href="#Lane8">Lane 8</a></td>
268 <h2><br></br>Lane Results Summary<br></br></h2>
269 <table border="1" cellpadding="5">
271 <td colspan="2">Lane Info</td>
272 <td colspan="8">Tile Mean +/- SD for Lane</td>
276 <td>Lane Yield (kbases) </td>
277 <td>Clusters (raw)</td>
278 <td>Clusters (PF) </td>
279 <td>1st Cycle Int (PF) </td>
280 <td>% intensity after 20 cycles (PF) </td>
281 <td>% PF Clusters </td>
282 <td>% Align (PF) </td>
283 <td>Alignment Score (PF) </td>
284 <td> % Error Rate (PF) </td>
289 <td>96483 +/- 9074</td>
290 <td>60787 +/- 4240</td>
292 <td>101.88 +/- 6.03</td>
293 <td>63.21 +/- 3.29</td>
294 <td>70.33 +/- 0.24</td>
295 <td>9054.08 +/- 59.16</td>
296 <td>0.46 +/- 0.18</td>
301 <td>133738 +/- 7938</td>
302 <td>60217 +/- 1926</td>
304 <td>92.62 +/- 7.58</td>
305 <td>45.20 +/- 3.31</td>
306 <td>51.98 +/- 0.74</td>
307 <td>6692.04 +/- 92.49</td>
308 <td>0.46 +/- 0.09</td>
313 <td>152142 +/- 10002</td>
314 <td>71468 +/- 2827</td>
316 <td>91.53 +/- 8.66</td>
317 <td>47.19 +/- 3.80</td>
318 <td>82.24 +/- 0.44</td>
319 <td>10598.68 +/- 64.13</td>
320 <td>0.41 +/- 0.04</td>
325 <td>15784 +/- 2162</td>
326 <td>13443 +/- 1728</td>
328 <td>97.53 +/- 9.87</td>
329 <td>85.29 +/- 1.91</td>
330 <td>80.02 +/- 0.53</td>
331 <td>10368.82 +/- 71.08</td>
332 <td>0.15 +/- 0.05</td>
337 <td>119735 +/- 8465</td>
338 <td>64590 +/- 2529</td>
340 <td>88.69 +/- 14.79</td>
341 <td>54.10 +/- 2.59</td>
342 <td>76.95 +/- 0.32</td>
343 <td>9936.47 +/- 65.75</td>
344 <td>0.28 +/- 0.02</td>
349 <td>152177 +/- 8146</td>
350 <td>66716 +/- 2493</td>
352 <td>87.06 +/- 9.86</td>
353 <td>43.98 +/- 3.12</td>
354 <td>78.80 +/- 0.43</td>
355 <td>10162.28 +/- 49.65</td>
356 <td>0.38 +/- 0.03</td>
361 <td>84649 +/- 7325</td>
362 <td>57418 +/- 3617</td>
364 <td>89.40 +/- 8.23</td>
365 <td>67.97 +/- 1.82</td>
366 <td>33.38 +/- 0.25</td>
367 <td>4247.92 +/- 32.37</td>
368 <td>1.00 +/- 0.03</td>
373 <td>54622 +/- 4812</td>
374 <td>41136 +/- 3309</td>
376 <td>90.21 +/- 9.10</td>
377 <td>75.39 +/- 2.27</td>
378 <td>48.33 +/- 0.29</td>
379 <td>6169.21 +/- 169.50</td>
380 <td>0.86 +/- 1.22</td>
382 <tr><td colspan="13">Tile mean across chip</td></tr>
396 <h2><br></br>Expanded Lane Summary<br></br></h2>
397 <table border="1" cellpadding="5">
400 <tr><td colspan="2">Lane Info</td>
401 <td colspan="2">Phasing Info</td>
402 <td colspan="2">Raw Data (tile mean)</td>
403 <td colspan="7">Filtered Data (tile mean)</td></tr>
405 <td>Clusters (tile mean) (raw)</td>
407 <td>% Prephasing </td>
408 <td>% Error Rate (raw) </td>
409 <td> Equiv Perfect Clusters (raw) </td>
411 <td>Cycle 2-4 Av Int (PF) </td>
412 <td>Cycle 2-10 Av % Loss (PF) </td>
413 <td>Cycle 10-20 Av % Loss (PF) </td>
414 <td>% Align (PF) </td>
415 <td>% Error Rate (PF) </td>
416 <td> Equiv Perfect Clusters (PF) </td>
427 <td>0.13 +/- 0.44</td>
428 <td>-1.14 +/- 0.34</td>
442 <td>0.29 +/- 0.40</td>
443 <td>-0.79 +/- 0.35</td>
457 <td>0.68 +/- 0.51</td>
458 <td>-0.77 +/- 0.42</td>
472 <td>0.20 +/- 0.69</td>
473 <td>-1.28 +/- 0.66</td>
487 <td>0.34 +/- 0.49</td>
488 <td>-1.55 +/- 4.69</td>
502 <td>0.57 +/- 0.50</td>
503 <td>-0.91 +/- 0.39</td>
517 <td>1.15 +/- 0.52</td>
518 <td>-0.84 +/- 0.58</td>
532 <td>1.10 +/- 0.59</td>
533 <td>-1.01 +/- 0.47</td>
539 <b><br></br>IVC Plots</b>
540 <p> <a href='IVC.htm' target="_blank"> IVC.htm
542 <b><br></br>All Intensity Plots</b>
543 <p> <a href='All.htm' target="_blank"> All.htm
545 <b><br></br>Error graphs: </b>
546 <p> <a href='Error.htm' target="_blank"> Error.htm
548 <td><a href="#Top">Back to top</a></td>
549 <a name="Lane1"><h2><br></br>Lane 1<br></br></h2></a>
550 <table border="1" cellpadding="5">
554 <td>Clusters (raw)</td>
555 <td>Av 1st Cycle Int (PF) </td>
556 <td>Av % intensity after 20 cycles (PF) </td>
557 <td>% PF Clusters </td>
558 <td>% Align (PF) </td>
559 <td>Av Alignment Score (PF) </td>
560 <td>% Error Rate (PF) </td>
574 <td><a href="#Top">Back to top</a></td>
575 <a name="Lane2"><h2><br></br>Lane 2<br></br></h2></a>
576 <table border="1" cellpadding="5">
580 <td>Clusters (raw)</td>
581 <td>Av 1st Cycle Int (PF) </td>
582 <td>Av % intensity after 20 cycles (PF) </td>
583 <td>% PF Clusters </td>
584 <td>% Align (PF) </td>
585 <td>Av Alignment Score (PF) </td>
586 <td>% Error Rate (PF) </td>
600 <td><a href="#Top">Back to top</a></td>
601 <a name="Lane3"><h2><br></br>Lane 3<br></br></h2></a>
602 <table border="1" cellpadding="5">
606 <td>Clusters (raw)</td>
607 <td>Av 1st Cycle Int (PF) </td>
608 <td>Av % intensity after 20 cycles (PF) </td>
609 <td>% PF Clusters </td>
610 <td>% Align (PF) </td>
611 <td>Av Alignment Score (PF) </td>
612 <td>% Error Rate (PF) </td>
626 <td><a href="#Top">Back to top</a></td>
627 <a name="Lane4"><h2><br></br>Lane 4<br></br></h2></a>
628 <table border="1" cellpadding="5">
632 <td>Clusters (raw)</td>
633 <td>Av 1st Cycle Int (PF) </td>
634 <td>Av % intensity after 20 cycles (PF) </td>
635 <td>% PF Clusters </td>
636 <td>% Align (PF) </td>
637 <td>Av Alignment Score (PF) </td>
638 <td>% Error Rate (PF) </td>
652 <td><a href="#Top">Back to top</a></td>
653 <a name="Lane5"><h2><br></br>Lane 5<br></br></h2></a>
654 <table border="1" cellpadding="5">
658 <td>Clusters (raw)</td>
659 <td>Av 1st Cycle Int (PF) </td>
660 <td>Av % intensity after 20 cycles (PF) </td>
661 <td>% PF Clusters </td>
662 <td>% Align (PF) </td>
663 <td>Av Alignment Score (PF) </td>
664 <td>% Error Rate (PF) </td>
667 <td><a href="#Top">Back to top</a></td>
668 <a name="Lane6"><h2><br></br>Lane 6<br></br></h2></a>
669 <table border="1" cellpadding="5">
673 <td>Clusters (raw)</td>
674 <td>Av 1st Cycle Int (PF) </td>
675 <td>Av % intensity after 20 cycles (PF) </td>
676 <td>% PF Clusters </td>
677 <td>% Align (PF) </td>
678 <td>Av Alignment Score (PF) </td>
679 <td>% Error Rate (PF) </td>
693 <td><a href="#Top">Back to top</a></td>
694 <a name="Lane7"><h2><br></br>Lane 7<br></br></h2></a>
695 <table border="1" cellpadding="5">
699 <td>Clusters (raw)</td>
700 <td>Av 1st Cycle Int (PF) </td>
701 <td>Av % intensity after 20 cycles (PF) </td>
702 <td>% PF Clusters </td>
703 <td>% Align (PF) </td>
704 <td>Av Alignment Score (PF) </td>
705 <td>% Error Rate (PF) </td>
719 <td><a href="#Top">Back to top</a></td>
720 <a name="Lane8"><h2><br></br>Lane 8<br></br></h2></a>
721 <table border="1" cellpadding="5">
725 <td>Clusters (raw)</td>
726 <td>Av 1st Cycle Int (PF) </td>
727 <td>Av % intensity after 20 cycles (PF) </td>
728 <td>% PF Clusters </td>
729 <td>% Align (PF) </td>
730 <td>Av Alignment Score (PF) </td>
731 <td>% Error Rate (PF) </td>
745 <td><a href="#Top">Back to top</a></td>
749 pathname = os.path.join(gerald_dir, 'Summary.htm')
750 f = open(pathname, 'w')
754 def make_eland_results(gerald_dir):
755 eland_result = """>HWI-EAS229_24_207BTAAXX:1:7:599:759 ACATAGNCACAGACATAAACATAGACATAGAC U0 1 1 3 chrUextra.fa 28189829 R D.
756 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 chr2L.fa 8796855 R DD 24T
757 >HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
758 >HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
761 pathname = os.path.join(gerald_dir,
762 's_%d_eland_result.txt' % (i,))
763 f = open(pathname, 'w')
764 f.write(eland_result)
767 def make_runfolder(obj=None):
769 Make a fake runfolder, attach all the directories to obj if defined
771 # make a fake runfolder directory
772 temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
774 runfolder_dir = os.path.join(temp_dir,
775 '080102_HWI-EAS229_0010_207BTAAXX')
776 os.mkdir(runfolder_dir)
778 data_dir = os.path.join(runfolder_dir, 'Data')
781 firecrest_dir = os.path.join(data_dir,
782 'C1-33_Firecrest1.8.28_12-04-2008_diane'
784 os.mkdir(firecrest_dir)
785 matrix_dir = os.path.join(firecrest_dir, 'Matrix')
787 make_matrix(matrix_dir)
789 bustard_dir = os.path.join(firecrest_dir,
790 'Bustard1.8.28_12-04-2008_diane')
791 os.mkdir(bustard_dir)
792 make_phasing_params(bustard_dir)
794 gerald_dir = os.path.join(bustard_dir,
795 'GERALD_12-04-2008_diane')
797 make_gerald_config(gerald_dir)
798 make_summary_htm(gerald_dir)
799 make_eland_results(gerald_dir)
802 obj.temp_dir = temp_dir
803 obj.runfolder_dir = runfolder_dir
804 obj.data_dir = data_dir
805 obj.firecrest_dir = firecrest_dir
806 obj.matrix_dir = matrix_dir
807 obj.bustard_dir = bustard_dir
808 obj.gerald_dir = gerald_dir
811 class RunfolderTests(unittest.TestCase):
813 Test components of the runfolder processing code
814 which includes firecrest, bustard, and gerald
817 # attaches all the directories to the object passed in
821 shutil.rmtree(self.temp_dir)
823 def test_firecrest(self):
825 Construct a firecrest object
827 f = firecrest.firecrest(self.firecrest_dir)
828 self.failUnlessEqual(f.version, '1.8.28')
829 self.failUnlessEqual(f.start, 1)
830 self.failUnlessEqual(f.stop, 33)
831 self.failUnlessEqual(f.user, 'diane')
832 self.failUnlessEqual(f.date, date(2008,4,12))
834 xml = f.get_elements()
835 # just make sure that element tree can serialize the tree
836 xml_str = ElementTree.tostring(xml)
838 f2 = firecrest.Firecrest(xml=xml)
839 self.failUnlessEqual(f.version, f2.version)
840 self.failUnlessEqual(f.start, f2.start)
841 self.failUnlessEqual(f.stop, f2.stop)
842 self.failUnlessEqual(f.user, f2.user)
843 self.failUnlessEqual(f.date, f2.date)
845 def test_bustard(self):
847 construct a bustard object
849 b = bustard.bustard(self.bustard_dir)
850 self.failUnlessEqual(b.version, '1.8.28')
851 self.failUnlessEqual(b.date, date(2008,4,12))
852 self.failUnlessEqual(b.user, 'diane')
853 self.failUnlessEqual(len(b.phasing), 8)
854 self.failUnlessAlmostEqual(b.phasing[8].phasing, 0.0099)
856 xml = b.get_elements()
857 b2 = bustard.Bustard(xml=xml)
858 self.failUnlessEqual(b.version, b2.version)
859 self.failUnlessEqual(b.date, b2.date )
860 self.failUnlessEqual(b.user, b2.user)
861 self.failUnlessEqual(len(b.phasing), len(b2.phasing))
862 for key in b.phasing.keys():
863 self.failUnlessEqual(b.phasing[key].lane,
864 b2.phasing[key].lane)
865 self.failUnlessEqual(b.phasing[key].phasing,
866 b2.phasing[key].phasing)
867 self.failUnlessEqual(b.phasing[key].prephasing,
868 b2.phasing[key].prephasing)
870 def test_gerald(self):
871 # need to update gerald and make tests for it
872 g = gerald.gerald(self.gerald_dir)
874 self.failUnlessEqual(g.version,
875 '@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp')
876 self.failUnlessEqual(g.date, datetime(2008,4,19,19,8,30))
877 self.failUnlessEqual(len(g.lanes), len(g.lanes.keys()))
878 self.failUnlessEqual(len(g.lanes), len(g.lanes.items()))
881 # list of genomes, matches what was defined up in
882 # make_gerald_config.
883 # the first None is to offset the genomes list to be 1..9
884 # instead of pythons default 0..8
885 genomes = [None, '/g/dm3', '/g/equcab1', '/g/equcab1', '/g/canfam2',
886 '/g/hg18', '/g/hg18', '/g/hg18', '/g/hg18', ]
888 # test lane specific parameters from gerald config file
890 cur_lane = g.lanes[str(i)]
891 self.failUnlessEqual(cur_lane.analysis, 'eland')
892 self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
893 self.failUnlessEqual(cur_lane.read_length, '32')
894 self.failUnlessEqual(cur_lane.use_bases, 'Y'*32)
896 # test data extracted from summary file
898 (96483, 9074), (133738, 7938),
899 (152142, 10002), (15784, 2162),
900 (119735, 8465), (152177, 8146),
901 (84649, 7325), (54622, 4812),]
904 summary_lane = g.summary[str(i)]
905 self.failUnlessEqual(summary_lane.cluster, clusters[i])
906 self.failUnlessEqual(summary_lane.lane, str(i))
908 xml = g.get_elements()
909 # just make sure that element tree can serialize the tree
910 xml_str = ElementTree.tostring(xml)
911 g2 = gerald.Gerald(xml=xml)
913 # do it all again after extracting from the xml file
914 self.failUnlessEqual(g.version, g2.version)
915 self.failUnlessEqual(g.date, g2.date)
916 self.failUnlessEqual(len(g.lanes.keys()), len(g2.lanes.keys()))
917 self.failUnlessEqual(len(g.lanes.items()), len(g2.lanes.items()))
919 # test lane specific parameters from gerald config file
921 g_lane = g.lanes[str(i)]
922 g2_lane = g2.lanes[str(i)]
923 self.failUnlessEqual(g_lane.analysis, g2_lane.analysis)
924 self.failUnlessEqual(g_lane.eland_genome, g2_lane.eland_genome)
925 self.failUnlessEqual(g_lane.read_length, g2_lane.read_length)
926 self.failUnlessEqual(g_lane.use_bases, g2_lane.use_bases)
928 # test (some) summary elements
930 g_summary = g.summary[str(i)]
931 g2_summary = g2.summary[str(i)]
932 self.failUnlessEqual(g_summary.cluster, g2_summary.cluster)
933 self.failUnlessEqual(g_summary.lane, g2_summary.lane)
935 g_eland = g.eland_results
936 g2_eland = g2.eland_results
937 for lane in g_eland.keys():
938 self.failUnlessEqual(g_eland[lane].reads,
939 g2_eland[lane].reads)
940 self.failUnlessEqual(len(g_eland[lane].mapped_reads),
941 len(g2_eland[lane].mapped_reads))
942 for k in g_eland[lane].mapped_reads.keys():
943 self.failUnlessEqual(g_eland[lane].mapped_reads[k],
944 g2_eland[lane].mapped_reads[k])
946 self.failUnlessEqual(len(g_eland[lane].match_codes),
947 len(g2_eland[lane].match_codes))
948 for k in g_eland[lane].match_codes.keys():
949 self.failUnlessEqual(g_eland[lane].match_codes[k],
950 g2_eland[lane].match_codes[k])
953 def test_eland(self):
954 dm3_map = { 'chrUextra.fa' : 'dm3/chrUextra.fa',
955 'chr2L.fa': 'dm3/chr2L.fa',
956 'Lambda.fa': 'Lambda.fa'}
957 genome_maps = { '1':dm3_map, '2':dm3_map, '3':dm3_map, '4':dm3_map,
958 '5':dm3_map, '6':dm3_map, '7':dm3_map, '8':dm3_map }
959 eland = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
963 self.failUnlessEqual(lane.reads, 4)
964 self.failUnlessEqual(lane.sample_name, "s")
965 self.failUnlessEqual(lane.lane_id, unicode(i))
966 self.failUnlessEqual(len(lane.mapped_reads), 3)
967 self.failUnlessEqual(lane.mapped_reads['Lambda.fa'], 1)
968 self.failUnlessEqual(lane.mapped_reads['dm3/chr2L.fa'], 1)
969 self.failUnlessEqual(lane.match_codes['U1'], 2)
970 self.failUnlessEqual(lane.match_codes['NM'], 1)
972 xml = eland.get_elements()
973 # just make sure that element tree can serialize the tree
974 xml_str = ElementTree.tostring(xml)
975 e2 = gerald.ELAND(xml=xml)
980 self.failUnlessEqual(l1.reads, l2.reads)
981 self.failUnlessEqual(l1.sample_name, l2.sample_name)
982 self.failUnlessEqual(l1.lane_id, l2.lane_id)
983 self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
984 self.failUnlessEqual(len(l1.mapped_reads), 3)
985 for k in l1.mapped_reads.keys():
986 self.failUnlessEqual(l1.mapped_reads[k],
989 self.failUnlessEqual(len(l1.match_codes), 9)
990 self.failUnlessEqual(len(l1.match_codes), len(l2.match_codes))
991 for k in l1.match_codes.keys():
992 self.failUnlessEqual(l1.match_codes[k],
995 def test_runfolder(self):
996 runs = runfolder.get_runs(self.runfolder_dir)
998 # do we get the flowcell id from the filename?
999 self.failUnlessEqual(len(runs), 1)
1000 self.failUnlessEqual(runs[0].name, 'run_207BTAAXX_2008-04-19.xml')
1002 # do we get the flowcell id from the FlowcellId.xml file
1003 make_flowcell_id(self.runfolder_dir, '207BTAAXY')
1004 runs = runfolder.get_runs(self.runfolder_dir)
1005 self.failUnlessEqual(len(runs), 1)
1006 self.failUnlessEqual(runs[0].name, 'run_207BTAAXY_2008-04-19.xml')
1009 xml = r1.get_elements()
1010 xml_str = ElementTree.tostring(xml)
1012 r2 = runfolder.PipelineRun(xml=xml)
1013 self.failUnlessEqual(r1.name, r2.name)
1014 self.failIfEqual(r2.firecrest, None)
1015 self.failIfEqual(r2.bustard, None)
1016 self.failIfEqual(r2.gerald, None)
1020 return unittest.makeSuite(RunfolderTests,'test')
1022 if __name__ == "__main__":
1023 unittest.main(defaultTest="suite")