+"""
+Extract configuration from Illumina Bustard Directory.
+This includes the version number, run date, bustard executable parameters, and
+phasing estimates.
+"""
+from copy import copy
from datetime import date
from glob import glob
import logging
import os
-import time
import re
+import sys
+import time
-from htsworkflow.pipelines.runfolder import \
+from htsworkflow.pipelines import \
ElementTree, \
VERSION_RE, \
EUROPEAN_STRPTIME
+LOGGER = logging.getLogger(__name__)
+
+# make epydoc happy
+__docformat__ = "restructuredtext en"
+
+LANE_LIST = list(range(1,9))
+
class Phasing(object):
PHASING = 'Phasing'
PREPHASING = 'Prephasing'
def get_elements(self):
root = ElementTree.Element(Phasing.PHASING, {'lane': str(self.lane)})
+ root.tail = os.linesep
phasing = ElementTree.SubElement(root, Phasing.PHASING)
phasing.text = str(self.phasing)
+ phasing.tail = os.linesep
prephasing = ElementTree.SubElement(root, Phasing.PREPHASING)
prephasing.text = str(self.prephasing)
+ prephasing.tail = os.linesep
return root
def set_elements(self, tree):
elif element.tag == Phasing.PREPHASING:
self.prephasing = float(element.text)
+class CrosstalkMatrix(object):
+ CROSSTALK = "MatrixElements"
+ BASE = 'Base'
+ ELEMENT = 'Element'
+
+ def __init__(self, fromfile=None, xml=None):
+ self.base = {}
+
+ if fromfile is not None:
+ self._initialize_from_file(fromfile)
+ elif xml is not None:
+ self.set_elements(xml)
+
+ def _initialize_from_file(self, pathname):
+ data = open(pathname).readlines()
+ auto_header = '# Auto-generated frequency response matrix'
+ if data[0].strip() == auto_header and len(data) == 9:
+ # skip over lines 1,2,3,4 which contain the 4 bases
+ self.base['A'] = [ float(v) for v in data[5].split() ]
+ self.base['C'] = [ float(v) for v in data[6].split() ]
+ self.base['G'] = [ float(v) for v in data[7].split() ]
+ self.base['T'] = [ float(v) for v in data[8].split() ]
+ elif len(data) == 16:
+ self.base['A'] = [ float(v) for v in data[:4] ]
+ self.base['C'] = [ float(v) for v in data[4:8] ]
+ self.base['G'] = [ float(v) for v in data[8:12] ]
+ self.base['T'] = [ float(v) for v in data[12:16] ]
+ else:
+ raise RuntimeError("matrix file %s is unusual" % (pathname,))
+ def get_elements(self):
+ root = ElementTree.Element(CrosstalkMatrix.CROSSTALK)
+ root.tail = os.linesep
+ base_order = ['A','C','G','T']
+ for b in base_order:
+ base_element = ElementTree.SubElement(root, CrosstalkMatrix.BASE)
+ base_element.text = b
+ base_element.tail = os.linesep
+ for b in base_order:
+ for value in self.base[b]:
+ crosstalk_value = ElementTree.SubElement(root, CrosstalkMatrix.ELEMENT)
+ crosstalk_value.text = str(value)
+ crosstalk_value.tail = os.linesep
+
+ return root
+
+ def set_elements(self, tree):
+ if tree.tag != CrosstalkMatrix.CROSSTALK:
+ raise ValueError('Invalid run-xml exptected '+CrosstalkMatrix.CROSSTALK)
+ base_order = []
+ current_base = None
+ current_index = 0
+ for element in tree.getchildren():
+ # read in the order of the bases
+ if element.tag == 'Base':
+ base_order.append(element.text)
+ elif element.tag == 'Element':
+ # we're done reading bases, now its just the 4x4 matrix
+ # written out as a list of elements
+ # if this is the first element, make a copy of the list
+ # to play with and initialize an empty list for the current base
+ if current_base is None:
+ current_base = copy(base_order)
+ self.base[current_base[0]] = []
+ # we found (probably) 4 bases go to the next base
+ if current_index == len(base_order):
+ current_base.pop(0)
+ current_index = 0
+ self.base[current_base[0]] = []
+ value = float(element.text)
+ self.base[current_base[0]].append(value)
+
+ current_index += 1
+ else:
+ raise RuntimeError("Unrecognized tag in run xml: %s" %(element.tag,))
+
+def crosstalk_matrix_from_bustard_config(bustard_path, bustard_config_tree):
+ """
+ Analyze the bustard config file and try to find the crosstalk matrix.
+ """
+ bustard_run = bustard_config_tree[0]
+ if bustard_run.tag != 'Run':
+ raise RuntimeError('Expected Run tag, got %s' % (bustard_run.tag,))
+
+ call_parameters = bustard_run.find('BaseCallParameters')
+ if call_parameters is None:
+ raise RuntimeError('Missing BaseCallParameters section')
+
+ matrix = call_parameters.find('Matrix')
+ if matrix is None:
+ raise RuntimeError('Expected to find Matrix in Bustard BaseCallParameters')
+
+ matrix_auto_flag = int(matrix.find('AutoFlag').text)
+ matrix_auto_lane = int(matrix.find('AutoLane').text)
+
+ crosstalk = None
+ if matrix_auto_flag:
+ # we estimated the matrix from something in this run.
+ # though we don't really care which lane it was
+ if matrix_auto_lane == 0:
+ # its defaulting to all of the lanes, so just pick one
+ auto_lane_fragment = "_1"
+ else:
+ auto_lane_fragment = "_%d" % ( matrix_auto_lane,)
+
+ for matrix_name in ['s%s_02_matrix.txt' % (auto_lane_fragment,),
+ 's%s_1_matrix.txt' % (auto_lane_fragment,),
+ ]:
+ matrix_path = os.path.join(bustard_path, 'Matrix', matrix_name)
+ if os.path.exists(matrix_path):
+ break
+ else:
+ raise RuntimeError("Couldn't find matrix for lane %d" % \
+ (matrix_auto_lane,))
+
+ crosstalk = CrosstalkMatrix(matrix_path)
+ else:
+ matrix_elements = call_parameters.find('MatrixElements')
+ # the matrix was provided
+ if matrix_elements is not None:
+ crosstalk = CrosstalkMatrix(xml=matrix_elements)
+ else:
+ # we have no crosstalk matrix?
+ pass
+
+ return crosstalk
+
class Bustard(object):
- XML_VERSION = 1
+ XML_VERSION = 2
# Xml Tags
BUSTARD = 'Bustard'
DATE = 'run_time'
USER = 'user'
PARAMETERS = 'Parameters'
+ BUSTARD_CONFIG = 'BaseCallAnalysis'
def __init__(self, xml=None):
- self.version = None
- self.date = date.today()
+ self._path_version = None # version number from directory name
+ self.date = None
self.user = None
self.phasing = {}
+ self.crosstalk = None
+ self.pathname = None
+ self.bustard_config = None
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._path_version = version.group(1)
+ t = time.strptime(groups[1], EUROPEAN_STRPTIME)
+ self.date = date(*t[0:3])
+ self.user = groups[2]
+
+ def _get_sequence_format(self):
+ """Guess sequence format"""
+ project_glob = os.path.join(self.pathname, 'Project_*')
+ LOGGER.debug("Scanning: %s" % (project_glob,))
+ projects = glob(project_glob)
+ if len(projects) > 0:
+ # Hey we look like a demultiplexed run
+ return 'fastq'
+ seqs = glob(os.path.join(self.pathname, '*_seq.txt'))
+ if len(seqs) > 0:
+ return 'srf'
+ return 'qseq'
+ sequence_format = property(_get_sequence_format)
+
+ def _get_software_version(self):
+ """return software name, version tuple"""
+ if self.bustard_config is None:
+ if self._path_version is not None:
+ return 'Bustard', self._path_version
+ else:
+ return None
+ software_nodes = self.bustard_config.xpath('Run/Software')
+ if len(software_nodes) == 0:
+ return None
+ elif len(software_nodes) > 1:
+ raise RuntimeError("Too many software XML elements for bustard.py")
+ else:
+ return (software_nodes[0].attrib['Name'],
+ software_nodes[0].attrib['Version'])
+
+ def _get_software(self):
+ """Return software name"""
+ software_version = self._get_software_version()
+ return software_version[0] if software_version is not None else None
+ software = property(_get_software)
+
+ def _get_version(self):
+ """Return software name"""
+ software_version = self._get_software_version()
+ return software_version[1] if software_version is not None else None
+ version = property(_get_version)
+
+
def _get_time(self):
+ if self.date is None:
+ return None
return time.mktime(self.date.timetuple())
time = property(_get_time, doc='return run time as seconds since epoch')
def dump(self):
- print "Bustard version:", self.version
- print "Run date", self.date
- print "user:", self.user
- for lane, tree in self.phasing.items():
- print lane
- print tree
+ #print ElementTree.tostring(self.get_elements())
+ ElementTree.dump(self.get_elements())
def get_elements(self):
- root = ElementTree.Element('Bustard',
+ root = ElementTree.Element('Bustard',
{'version': str(Bustard.XML_VERSION)})
version = ElementTree.SubElement(root, Bustard.SOFTWARE_VERSION)
version.text = self.version
- run_date = ElementTree.SubElement(root, Bustard.DATE)
- run_date.text = str(self.time)
- user = ElementTree.SubElement(root, Bustard.USER)
- user.text = self.user
+ if self.time is not None:
+ run_date = ElementTree.SubElement(root, Bustard.DATE)
+ run_date.text = str(self.time)
+ if self.user is not None:
+ user = ElementTree.SubElement(root, Bustard.USER)
+ user.text = self.user
params = ElementTree.SubElement(root, Bustard.PARAMETERS)
- for p in self.phasing.values():
- params.append(p.get_elements())
+
+ # add phasing parameters
+ for lane in LANE_LIST:
+ if lane in self.phasing:
+ params.append(self.phasing[lane].get_elements())
+
+ # add crosstalk matrix if it exists
+ if self.crosstalk is not None:
+ root.append(self.crosstalk.get_elements())
+
+ # add bustard config if it exists
+ if self.bustard_config is not None:
+ root.append(self.bustard_config)
return root
def set_elements(self, tree):
raise ValueError('Expected "Bustard" SubElements')
xml_version = int(tree.attrib.get('version', 0))
if xml_version > Bustard.XML_VERSION:
- logging.warn('Bustard XML tree is a higher version than this class')
+ LOGGER.warn('Bustard XML tree is a higher version than this class')
for element in list(tree):
if element.tag == Bustard.SOFTWARE_VERSION:
- self.version = element.text
+ self._path_version = element.text
elif element.tag == Bustard.DATE:
self.date = date.fromtimestamp(float(element.text))
elif element.tag == Bustard.USER:
for param in element:
p = Phasing(xml=param)
self.phasing[p.lane] = p
+ elif element.tag == CrosstalkMatrix.CROSSTALK:
+ self.crosstalk = CrosstalkMatrix(xml=element)
+ elif element.tag == Bustard.BUSTARD_CONFIG:
+ self.bustard_config = element
else:
raise ValueError("Unrecognized tag: %s" % (element.tag,))
-
-
def bustard(pathname):
"""
- Construct a Bustard object from pathname
+ Construct a Bustard object by analyzing an Illumina Bustard directory.
+
+ :Parameters:
+ - `pathname`: A bustard directory
+
+ :Return:
+ Fully initialized Bustard object.
+ """
+ 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)
+
+ if not b:
+ raise RuntimeError("Unable to parse base-call directory at %s" % (pathname,))
+
+ return b
+
+def bustard_from_ga1(pathname):
+ """Initialize bustard class from ga1 era runfolders.
"""
- b = Bustard()
path, name = os.path.split(pathname)
+
groups = name.split("_")
+ if len(groups) < 3:
+ msg = "Not enough information to create attributes"\
+ " from directory name: %s"
+ LOGGER.error(msg % (pathname,))
+ return None
+
+ b = Bustard()
+ b.pathname = pathname
+ b.update_attributes_from_pathname()
version = re.search(VERSION_RE, groups[0])
- b.version = version.group(1)
+ b._path_version = version.group(1)
t = time.strptime(groups[1], EUROPEAN_STRPTIME)
b.date = date(*t[0:3])
b.user = groups[2]
- paramfiles = glob(os.path.join(pathname, "params?.xml"))
+
+ # 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.
+
+ # 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)
+ 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()
+ 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)
- b.phasing[phasing.lane] = phasing
- return b
+ bustard_obj.phasing[phasing.lane] = phasing
def fromxml(tree):
+ """
+ Reconstruct a htsworkflow.pipelines.Bustard object from an xml block
+ """
b = Bustard()
b.set_elements(tree)
return b
+
+def make_cmdline_parser():
+ from optparse import OptionParser
+ parser = OptionParser('%prog: bustard_directory')
+ return parser
+
+def main(cmdline):
+ parser = make_cmdline_parser()
+ opts, args = parser.parse_args(cmdline)
+
+ for bustard_dir in args:
+ print('analyzing bustard directory: ' + str(bustard_dir))
+ bustard_object = bustard(bustard_dir)
+ bustard_object.dump()
+
+ bustard_object2 = Bustard(xml=bustard_object.get_elements())
+ print ('-------------------------------------')
+ bustard_object2.dump()
+ print ('=====================================')
+ b1_tree = bustard_object.get_elements()
+ b1 = ElementTree.tostring(b1_tree).split(os.linesep)
+ b2_tree = bustard_object2.get_elements()
+ b2 = ElementTree.tostring(b2_tree).split(os.linesep)
+ for line1, line2 in zip(b1, b2):
+ if b1 != b2:
+ print("b1: ", b1)
+ print("b2: ", b2)
+
+if __name__ == "__main__":
+ main(sys.argv[1:])
projects / htsworkflow.git / blobdiff