if xml is not None:
self.set_elements(xml)
+ def update_attributes_from_pathname(self):
+ """Update version, date, user from bustard directory names
+ Obviously this wont work for BaseCalls or later runfolders
+ """
+ if self.pathname is None:
+ raise ValueError(
+ "Set pathname before calling update_attributes_from_pathname")
+ path, name = os.path.split(self.pathname)
+
+ if not re.match('bustard', name, re.IGNORECASE):
+ return
+
+ groups = name.split("_")
+ version = re.search(VERSION_RE, groups[0])
+ self.version = version.group(1)
+ t = time.strptime(groups[1], EUROPEAN_STRPTIME)
+ self.date = date(*t[0:3])
+ self.user = groups[2]
+
def _get_time(self):
if self.date is None:
return None
:Return:
Fully initialized Bustard object.
"""
- b = Bustard()
pathname = os.path.abspath(pathname)
+ bustard_filename = os.path.join(pathname, 'config.xml')
+ demultiplexed_filename = os.path.join(pathname,
+ 'DemultiplexedBustardConfig.xml')
+
+ if os.path.exists(demultiplexed_filename):
+ b = bustard_from_hiseq(pathname, demultiplexed_filename)
+ elif os.path.exists(bustard_filename):
+ b = bustard_from_ga2(pathname, bustard_filename)
+ else:
+ b = bustard_from_ga1(pathname)
+
+ return b
+
+def bustard_from_ga1(pathname):
+ """Initialize bustard class from ga1 era runfolders.
+ """
path, name = os.path.split(pathname)
+
groups = name.split("_")
- if groups[0].lower().startswith('bustard'):
- version = re.search(VERSION_RE, groups[0])
- b.version = version.group(1)
- t = time.strptime(groups[1], EUROPEAN_STRPTIME)
- b.date = date(*t[0:3])
- b.user = groups[2]
- elif groups[0] == 'BaseCalls':
- # stub values
- b.version = None
- b.date = None
- b.user = None
+ if len(groups) < 3:
+ msg = "Not enough information to create attributes"\
+ " from directory name: %s"
+ LOGGER.error(msg % (self.pathname,))
+ return None
+ b = Bustard()
b.pathname = pathname
- bustard_config_filename = os.path.join(pathname, 'config.xml')
- paramfiles = glob(os.path.join(pathname, "params?.xml"))
- for paramfile in paramfiles:
- phasing = Phasing(paramfile)
- assert (phasing.lane >= 1 and phasing.lane <= 8)
- b.phasing[phasing.lane] = phasing
+ b.update_attributes_from_pathname()
+ version = re.search(VERSION_RE, groups[0])
+ b.version = version.group(1)
+ t = time.strptime(groups[1], EUROPEAN_STRPTIME)
+ b.date = date(*t[0:3])
+ b.user = groups[2]
+
# I only found these in Bustard1.9.5/1.9.6 directories
if b.version in ('1.9.5', '1.9.6'):
# at least for our runfolders for 1.9.5 and 1.9.6 matrix[1-8].txt are always the same
crosstalk_file = os.path.join(pathname, "matrix1.txt")
b.crosstalk = CrosstalkMatrix(crosstalk_file)
+
+ add_phasing(b)
+ return b
+
+
+def bustard_from_ga2(pathname, config_filename):
+ """Initialize bustard class from ga2-era runfolder
+ Actually I don't quite remember if it is exactly the GA2s, but
+ its after the original runfolder style and before the HiSeq.
+ """
# for version 1.3.2 of the pipeline the bustard version number went down
# to match the rest of the pipeline. However there's now a nifty
# new (useful) bustard config file.
- elif os.path.exists(bustard_config_filename):
- bustard_config_root = ElementTree.parse(bustard_config_filename)
- b.bustard_config = bustard_config_root.getroot()
- b.crosstalk = crosstalk_matrix_from_bustard_config(b.pathname, b.bustard_config)
- software = bustard_config_root.find('*/Software')
- b.version = software.attrib['Version']
- #b.version = software.attrib['Name'] + "-" + software.attrib['Version']
+
+ # stub values
+ b = Bustard()
+ b.pathname = pathname
+ b.update_attributes_from_pathname()
+ bustard_config_root = ElementTree.parse(config_filename)
+ b.bustard_config = bustard_config_root.getroot()
+ b.crosstalk = crosstalk_matrix_from_bustard_config(b.pathname,
+ b.bustard_config)
+ software = bustard_config_root.find('*/Software')
+ b.version = software.attrib['Version']
+ add_phasing(b)
return b
+def bustard_from_hiseq(pathname, config_filename):
+ b = Bustard()
+ b.pathname = pathname
+ bustard_config_root = ElementTree.parse(config_filename)
+ b.bustard_config = bustard_config_root.getroot()
+ software = bustard_config_root.find('*/Software')
+ b.version = software.attrib['Version']
+ add_phasing(b)
+ return b
+
+def add_phasing(bustard_obj):
+ paramfiles = glob(os.path.join(bustard_obj.pathname,
+ "params?.xml"))
+ for paramfile in paramfiles:
+ phasing = Phasing(paramfile)
+ assert (phasing.lane >= 1 and phasing.lane <= 8)
+ bustard_obj.phasing[phasing.lane] = phasing
+
def fromxml(tree):
"""
Reconstruct a htsworkflow.pipelines.Bustard object from an xml block
if self.tree is None:
return None
- root = self._get_experiment_root()
- if root is None:
- root = ''
- else:
- root = os.path.join(root,'')
-
- experiment_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR')
- if experiment_dir is not None:
- experiment_dir = experiment_dir.replace(root, '')
- experiment_dir = self.tree.findtext('Defaults/EXPT_DIR')
- if experiment_dir is not None:
- _, experiment_dir = os.path.split(experiment_dir)
+ expt_root = os.path.normpath(self._get_experiment_root())
+ chip_expt_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR')
+ # hiseqs renamed the experiment dir location
+ defaults_expt_dir = self.tree.findtext('Defaults/EXPT_DIR')
+
+ experiment_dir = None
+ if defaults_expt_dir is not None:
+ _, experiment_dir = os.path.split(defaults_expt_dir)
+ elif expt_root is not None and chip_expt_dir is not None:
+ experiment_dir = chip_expt_dir.replace(expt_root+os.path.sep, '')
+ experiment_dir = experiment_dir.split(os.path.sep)[0]
+
if experiment_dir is None or len(experiment_dir) == 0:
return None
+ return experiment_dir
- dirnames = experiment_dir.split(os.path.sep)
- return dirnames[0]
runfolder_name = property(_get_runfolder_name)
def _get_version(self):
if self.tree is None:
return None
- return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
+ ga_version = self.tree.findtext(
+ 'ChipWideRunParameters/SOFTWARE_VERSION')
+ if ga_version is not None:
+ return ga_version
+ hiseq_software_node = self.tree.find('Software')
+ hiseq_version = hiseq_software_node.attrib['Version']
+ return hiseq_version
+
version = property(_get_version)
def _get_chip_attribute(self, value):
for bustard_pathname in bustard_dirs:
LOGGER.info("Found bustard directory %s" % (bustard_pathname,))
b = bustard.bustard(bustard_pathname)
- gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
- LOGGER.info("Looking for gerald directories in %s" % (pathname,))
- for gerald_pathname in glob(gerald_glob):
- LOGGER.info("Found gerald directory %s" % (gerald_pathname,))
- try:
- g = gerald.gerald(gerald_pathname)
- p = PipelineRun(runfolder, flowcell_id)
- p.datadir = datadir
- p.image_analysis = image_analysis
- p.bustard = b
- p.gerald = g
- runs.append(p)
- except IOError, e:
- LOGGER.error("Ignoring " + str(e))
-
- aligned_glob = os.path.join(runfolder, 'Aligned*')
- for aligned in glob(aligned_glob):
- LOGGER.info("Found aligned directory %s" % (aligned,))
- try:
- g = gerald.gerald(aligned)
- p = PipelineRun(runfolder, flowcell_id)
- p.datadir = datadir
- p.image_analysis = image_analysis
- p.bustard = b
- p.gerald = g
- runs.append(p)
- except IOError, e:
- LOGGER.error("Ignoring " + str(e))
+ build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder)
+
+ build_aligned_runs(image_analysis, runs, b, datadir, runfolder)
+
+ def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathname, runfolder):
+ gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
+ LOGGER.info("Looking for gerald directories in %s" % (pathname,))
+ for gerald_pathname in glob(gerald_glob):
+ LOGGER.info("Found gerald directory %s" % (gerald_pathname,))
+ try:
+ g = gerald.gerald(gerald_pathname)
+ p = PipelineRun(runfolder, flowcell_id)
+ p.datadir = datadir
+ p.image_analysis = image_analysis
+ p.bustard = b
+ p.gerald = g
+ runs.append(p)
+ except IOError, e:
+ LOGGER.error("Ignoring " + str(e))
+
+
+ def build_aligned_runs(image_analysis, runs, b, datadir, runfolder):
+ aligned_glob = os.path.join(runfolder, 'Aligned*')
+ for aligned in glob(aligned_glob):
+ LOGGER.info("Found aligned directory %s" % (aligned,))
+ try:
+ g = gerald.gerald(aligned)
+ p = PipelineRun(runfolder, flowcell_id)
+ p.datadir = datadir
+ p.image_analysis = image_analysis
+ p.bustard = b
+ p.gerald = g
+ runs.append(p)
+ except IOError, e:
+ LOGGER.error("Ignoring " + str(e))
datadir = os.path.join(runfolder, 'Data')
)
else:
scan_post_image_analysis(
- runs, runfolder, image_analysis, firecrest_pathname
+ runs, runfolder, datadir, image_analysis, firecrest_pathname
)
# scan for IPAR directories
ipar_dirs = glob(os.path.join(datadir, "IPAR_*"))
(os.path.join(TESTDATA_DIR, 'demultiplex_1.12.4.2.xml'),
os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
(os.path.join(TESTDATA_DIR, 'demultiplexed_bustard_1.12.4.2.xml'),
- os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
+ os.path.join(unaligned_dir, 'DemultiplexedBustardConfig.xml')),
(os.path.join(TESTDATA_DIR, 'demultiplexed_summary_1.12.4.2.xml'),
- os.path.join(unaligned_dir, 'DemultiplexConfig.xml')),
+ os.path.join(unaligned_dir, 'DemultiplexedBustardSummary.xml')),
]
for src, dest in demultiplex_pairs:
shutil.copy(src, dest)
destination = os.path.join(gerald_dir, 'Summary.xml')
shutil.copy(source, destination)
+def make_summary_rta1_12(status_dir):
+ source = os.path.join(TESTDATA_DIR, 'Summary-rta1_12.htm')
+ destination = os.path.join(status_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.
#!/usr/bin/env python
from datetime import datetime, date
+import logging
import os
import tempfile
import shutil
intensities_dir = make_rta_intensities_1_12(data_dir)
+ status_dir = os.path.join(data_dir, 'Status_Files')
+ os.mkdir(status_dir)
+ make_summary_rta1_12(status_dir)
+
basecalls_dir = make_rta_basecalls_1_12(intensities_dir)
make_matrix_dir_rta_1_12(basecalls_dir)
def test_bustard(self):
"""Construct a bustard object"""
b = bustard.bustard(self.bustard_dir)
- self.failUnlessEqual(b.version, '1.8.70.0')
+ self.failUnlessEqual(b.version, '1.12.4.2')
self.failUnlessEqual(b.date, None)
self.failUnlessEqual(b.user, None)
self.failUnlessEqual(len(b.phasing), 0)
# need to update gerald and make tests for it
g = gerald.gerald(self.gerald_dir)
- self.failUnlessEqual(g.version,
- '@(#) Id: GERALD.pl,v 1.171 2008/05/19 17:36:14 mzerara Exp')
- self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
+ self.failUnlessEqual(g.version, 'CASAVA-1.8.1')
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
return unittest.makeSuite(RunfolderTests,'test')
if __name__ == "__main__":
- #unittest.main(defaultTest="suite")
- class Test(object): pass
- t = Test()
- make_runfolder(t)
- print ('path ' + t.runfolder_dir)
+ logging.basicConfig(level=logging.WARN)
+ unittest.main(defaultTest="suite")
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\r
+<head>\r
+ <link rel="stylesheet" href="./Status.css" type="text/css" media="screen"/>\r
+ <script src="./Status.js" type="text/javascript"></script>\r
+ <script src="./Summary.js" type="text/javascript"></script>\r
+ <title>Status</title>\r
+</head>\r
+ \r
+<body>\r
+ <table style="border:none"><tr>\r
+ <td><img alt="Refresh" title="Refresh" name="RefreshBtn" height="25" width="25" src="./RefreshBtn/r1.png" onmouseout="this.src='./RefreshBtn/r1.png'" onmouseover="this.src='./RefreshBtn/r2.png'" onmousedown="this.src='./RefreshBtn/r3.png'" onmouseup="this.src='./RefreshBtn/r2.png'" onclick="window.location.reload(true)" /> </td>\r
+ <td id="StatUpdateDiv" >\r
+ <table class="StatusTable"><tr>\r
+ <th>Total:</th><td>0</td><th>Extracted:</th><td>0</td><th>Called:</th><td>0</td>\r
+ <th>Scored:</th><td>0</td><th>Copied:</th><td>0</td><th>Err.Rated:</th><td>0</td>\r
+ </tr></table></td> \r
+ <td id="RunNameTD">Loading Run Data ...</td>\r
+ </tr></table>\r
+ <script type="text/javascript">\r
+ loadXSLTable('../reports/StatusUpdate.xml', './StatusUpdate.xsl', 'StatUpdateDiv');\r
+ runName = xslTransform(loadXMLDoc('../reports/Status.xml'), loadXMLDoc('./RunName.xsl'));\r
+ document.getElementById("RunNameTD").innerHTML = runName;\r
+ document.title = runName + " Status";\r
+ </script>\r
+<ul id="tabmenu">\r
+ <li><a href="./RunInfo.htm">Run Info</a></li>\r
+ <li><a href="../Status.htm">Tile Status</a></li>\r
+ <li><a href="./Charts.htm">Charts</a></li>\r
+ <li><a class="selected" href="./Summary.htm">Summary</a></li>\r
+ <li><a class="space">Plots:</a></li>\r
+ <li><a href="./ByLane.htm">Cluster Density</a></li>\r
+ <li><a href="./ByCycle.htm">Data By Cycle</a></li>\r
+</ul>\r
+ \r
+<div id="container">\r
+ <div id="SumTbl1" ><p> No data available yet.</p></div>\r
+ <div id="SumTbl2"></div>\r
+ <div id="SumTbl3"></div>\r
+ <div id="SumTbl4"></div>\r
+ <div id="SumTbl5"></div>\r
+ <div id="SumTbl6"></div>\r
+ <div id="SumTbl7"></div>\r
+ <div id="SumTbl8"></div>\r
+ <div id="SumTbl9"></div>\r
+ <div id="SumTbl10"></div>\r
+ <div id="SumTbl11"></div>\r
+ <script type="text/javascript">loadSumTable()</script>\r
+</div>\r
+ \r
+</body>\r
+</html>\r
+\r
projects / htsworkflow.git / commitdiff