from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines.test.simulate_runfolder import *
-def make_flowcell_id(runfolder_dir, flowcell_id=None):
- if flowcell_id is None:
- flowcell_id = '207BTAAXY'
-
- config = """<?xml version="1.0"?>
-<FlowcellId>
- <Text>%s</Text>
-</FlowcellId>""" % (flowcell_id,)
- config_dir = os.path.join(runfolder_dir, 'Config')
-
- if not os.path.exists(config_dir):
- os.mkdir(config_dir)
- pathname = os.path.join(config_dir, 'FlowcellId.xml')
- f = open(pathname,'w')
- f.write(config)
- f.close()
-
-def make_matrix(matrix_dir):
- contents = """# Auto-generated frequency response matrix
-> A
-> C
-> G
-> T
-0.77 0.15 -0.04 -0.04
-0.76 1.02 -0.05 -0.06
--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.write(contents)
- f.close()
-
-def make_phasing_params(bustard_dir):
- for lane in range(1,9):
- pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
- f = open(pathname, 'w')
- f.write("""<Parameters>
- <Phasing>0.009900</Phasing>
- <Prephasing>0.003500</Prephasing>
-</Parameters>
-""")
- 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_summary_htm(gerald_dir):
summary_htm = """<!--RUN_TIME Mon Apr 21 11:52:25 2008 -->
r2 = runfolder.PipelineRun(xml=xml)
self.failUnlessEqual(r1.name, r2.name)
- self.failIfEqual(r2.firecrest, None)
+ self.failIfEqual(r2.image_analysis, None)
self.failIfEqual(r2.bustard, None)
self.failIfEqual(r2.gerald, None)
projects / htsworkflow.git / blobdiff