def _initialize_from_file(self, pathname):
data = open(pathname).readlines()
auto_header = '# Auto-generated frequency response matrix'
- if data[0].strip() != auto_header or len(data) != 9:
+ 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,))
- # 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() ]
-
def get_elements(self):
root = ElementTree.Element(CrosstalkMatrix.CROSSTALK)
root.tail = os.linesep
if matrix_auto_flag:
# we estimated the matrix from something in this run.
# though we don't really care which lane it was
- matrix_path = os.path.join(bustard_path, 'Matrix', 's_02_matrix.txt')
+ if matrix_auto_lane == 0:
+ matrix_path = os.path.join(bustard_path,
+ 'Matrix', 's_02_matrix.txt')
+ else:
+ matrix_path = os.path.join(bustard_path, 'Matrix',
+ 's_%d_1_matrix.txt' % (matrix_auto_lane,))
crosstalk = CrosstalkMatrix(matrix_path)
else:
matrix_elements = call_parameters.find('MatrixElements')
import os
import re
import stat
+import sys
from htsworkflow.pipelines.runfolder import ElementTree, LANE_LIST
from htsworkflow.util.ethelp import indent, flatten
ELAND_EXTENDED = 2
ELAND_EXPORT = 3
-
class ResultLane(object):
"""
Base class for result lanes
"""
XML_VERSION = 2
LANE = "ElandLane"
+ MATCH_COUNTS_RE = re.compile("([\d]+):([\d]+):([\d]+)")
+ DESCRIPTOR_MISMATCH_RE = re.compile("[AGCT]")
+ DESCRIPTOR_INDEL_RE = re.compile("^[\dAGCT]$")
+ SCORE_UNRECOGNIZED = 0
+ SCORE_QC = 1
+ SCORE_READ = 2
def __init__(self, pathname=None, lane_id=None, end=None, genome_map=None, eland_type=None, xml=None):
super(ElandLane, self).__init__(pathname, lane_id, end)
logging.info("summarizing results for %s" % (self.pathname))
+ stream = autoopen(self.pathname, 'r')
if self.eland_type == ELAND_SINGLE:
- result = self._update_eland_result(self.pathname)
+ result = self._update_eland_result(stream)
elif self.eland_type == ELAND_MULTI or \
self.eland_type == ELAND_EXTENDED:
- result = self._update_eland_multi(self.pathname)
+ result = self._update_eland_multi(stream)
+ elif self.eland_type == ELAND_EXPORT:
+ result = self._update_eland_export(stream)
else:
raise NotImplementedError("Only support single/multi/extended eland files")
self._match_codes, self._mapped_reads, self._reads = result
- def _update_eland_result(self, pathname):
+ def _update_eland_result(self, instream):
reads = 0
mapped_reads = {}
'U0':0, 'U1':0, 'U2':0,
'R0':0, 'R1':0, 'R2':0,
}
- for line in autoopen(pathname,'r'):
+ for line in instream:
reads += 1
fields = line.split()
# code = fields[2]
mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
return match_codes, mapped_reads, reads
- def _update_eland_multi(self, pathname):
+ def _update_eland_multi(self, instream):
+ """Summarize an eland_extend."""
+ MATCH_INDEX = 2
+ LOCATION_INDEX = 3
reads = 0
mapped_reads = {}
'U0':0, 'U1':0, 'U2':0,
'R0':0, 'R1':0, 'R2':0,
}
- match_counts_re = re.compile("([\d]+):([\d]+):([\d]+)")
- for line in autoopen(pathname,'r'):
+ for line in instream:
reads += 1
fields = line.split()
# fields[2] = QC/NM/or number of matches
- groups = match_counts_re.match(fields[2])
- if groups is None:
- match_codes[fields[2]] += 1
- else:
- # when there are too many hit, eland writes a - where
+ score_type = self._score_mapped_mismatches(fields[MATCH_INDEX],
+ match_codes)
+ if score_type == ElandLane.SCORE_READ:
+ # when there are too many hits, eland writes a - where
# it would have put the list of hits.
# or in a different version of eland, it just leaves
# that column blank, and only outputs 3 fields.
- if len(fields) < 4 or fields[3] == '-':
+ if len(fields) < 4 or fields[LOCATION_INDEX] == '-':
continue
- zero_mismatches = int(groups.group(1))
- if zero_mismatches == 1:
- match_codes['U0'] += 1
- elif zero_mismatches < 255:
- match_codes['R0'] += zero_mismatches
-
- one_mismatches = int(groups.group(2))
- if one_mismatches == 1:
- match_codes['U1'] += 1
- elif one_mismatches < 255:
- match_codes['R1'] += one_mismatches
-
- two_mismatches = int(groups.group(3))
- if two_mismatches == 1:
- match_codes['U2'] += 1
- elif two_mismatches < 255:
- match_codes['R2'] += two_mismatches
-
- chromo = None
- for match in fields[3].split(','):
- match_fragment = match.split(':')
- if len(match_fragment) == 2:
- chromo = match_fragment[0]
- pos = match_fragment[1]
-
- fasta = self.genome_map.get(chromo, chromo)
- assert fasta is not None
- mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
+
+ self._count_mapped_multireads(mapped_reads, fields[LOCATION_INDEX])
+
return match_codes, mapped_reads, reads
+ def _update_eland_export(self, instream):
+ """Summarize a gerald export file."""
+ MATCH_INDEX = 10
+ LOCATION_INDEX = 10
+ DESCRIPTOR_INDEX= 13
+ reads = 0
+ mapped_reads = {}
+
+ match_codes = {'NM':0, 'QC':0, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ }
+
+ for line in instream:
+ reads += 1
+ fields = line.split()
+ # fields[2] = QC/NM/or number of matches
+ score_type = self._score_mapped_mismatches(fields[MATCH_INDEX],
+ match_codes)
+ if score_type == ElandLane.SCORE_UNRECOGNIZED:
+ # export files have three states for the match field
+ # QC code, count of multi-reads, or a single
+ # read location. The score_mapped_mismatches function
+ # only understands the first two types.
+ # if we get unrecognized, that implies the field is probably
+ # a location.
+ code = self._count_mapped_export(mapped_reads,
+ fields[LOCATION_INDEX],
+ fields[DESCRIPTOR_INDEX])
+ match_codes[code] += 1
+
+ return match_codes, mapped_reads, reads
+
+
+ def _score_mapped_mismatches(self, match, match_codes):
+ """Update match_codes with eland map counts, or failure code.
+
+ Returns True if the read mapped, false if it was an error code.
+ """
+ groups = ElandLane.MATCH_COUNTS_RE.match(match)
+ if groups is None:
+ # match is not of the form [\d]+:[\d]+:[\d]+
+ if match_codes.has_key(match):
+ # match is one quality control codes QC/NM etc
+ match_codes[match] += 1
+ return ElandLane.SCORE_QC
+ else:
+ return ElandLane.SCORE_UNRECOGNIZED
+ else:
+ # match is of the form [\d]+:[\d]+:[\d]+
+ # AKA Multiread
+ zero_mismatches = int(groups.group(1))
+ one_mismatches = int(groups.group(2))
+ two_mismatches = int(groups.group(3))
+
+ if zero_mismatches == 1:
+ match_codes['U0'] += 1
+ elif zero_mismatches < 255:
+ match_codes['R0'] += zero_mismatches
+
+ if one_mismatches == 1:
+ match_codes['U1'] += 1
+ elif one_mismatches < 255:
+ match_codes['R1'] += one_mismatches
+
+ if two_mismatches == 1:
+ match_codes['U2'] += 1
+ elif two_mismatches < 255:
+ match_codes['R2'] += two_mismatches
+
+ return ElandLane.SCORE_READ
+
+
+ def _count_mapped_multireads(self, mapped_reads, match_string):
+ chromo = None
+ for match in match_string.split(','):
+ match_fragment = match.split(':')
+ if len(match_fragment) == 2:
+ chromo = match_fragment[0]
+ pos = match_fragment[1]
+
+ fasta = self.genome_map.get(chromo, chromo)
+ assert fasta is not None
+ mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
+
+
+ def _count_mapped_export(self, mapped_reads, match_string, descriptor):
+ """Count a read as defined in an export file
+
+ match_string contains the chromosome
+ descriptor contains the an ecoding of bases that match, mismatch,
+ and have indels.
+ returns the "best" match code
+
+ Currently "best" match code is ignoring the possibility of in-dels
+ """
+ chromo = match_string
+ fasta = self.genome_map.get(chromo, chromo)
+ assert fasta is not None
+ mapped_reads[fasta] = mapped_reads.setdefault(fasta, 0) + 1
+
+ mismatch_bases = ElandLane.DESCRIPTOR_MISMATCH_RE.findall(descriptor)
+ if len(mismatch_bases) == 0:
+ return 'U0'
+ elif len(mismatch_bases) == 1:
+ return 'U1'
+ else:
+ return 'U2'
+
+
def _get_mapped_reads(self):
if self._mapped_reads is None:
self._update()
full_lane_id = "%d_%d" % ( lane_id, end )
basename = pattern % (full_lane_id,)
+ logging.info("Eland pattern: %s" %(basename,))
pathname = os.path.join(basedir, basename)
if os.path.exists(pathname):
logging.info('found eland file in %s' % (pathname,))
('s_%s_eland_multi.txt', MAPPED_ELAND),
('s_%s_eland_multi.txt.bz2', MAPPED_ELAND),
('s_%s_eland_multi.txt.gz', MAPPED_ELAND),
+ ('s_%s_export.txt', MAPPED_ELAND),
+ ('s_%s_export.txt.bz2', MAPPED_ELAND),
+ ('s_%s_export.txt.gz', MAPPED_ELAND),
('s_%s_sequence.txt', SEQUENCE),]
for basedir in basedirs:
result = [record[0][start:end]]
outstream.write("\t".join(result))
outstream.write(os.linesep)
+
+
+def main(cmdline=None):
+ """Run eland extraction against the specified gerald directory"""
+ from optparse import OptionParser
+ parser = OptionParser("%prog: <gerald dir>+")
+ opts, args = parser.parse_args(cmdline)
+ logging.basicConfig(level=logging.DEBUG)
+ for a in args:
+ logging.info("Starting scan of %s" % (a,))
+ e = eland(a)
+ print e.get_elements()
+
+ return
+
+
+if __name__ == "__main__":
+ main(sys.argv[1:])
return basecalls_dir
+def make_rta_intensities_1870(data_dir, version='1.8.70.0'):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ intensities_dir = os.path.join(data_dir, 'Intensities')
+ if not os.path.exists(intensities_dir):
+ os.mkdir(intensities_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config_1870.xml')
+ shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
+
+ return intensities_dir
+
+def make_rta_basecalls_1870(intensities_dir):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
+ if not os.path.exists(basecalls_dir):
+ os.mkdir(basecalls_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config_1870.xml')
+ shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
+
+ return basecalls_dir
+
def make_qseqs(bustard_dir, in_temp=True):
"""
Fill gerald directory with qseq files
f.write(contents)
f.close()
+def make_matrix_dir_rta160(bustard_dir):
+ """
+ Create several matrix files in <bustard_dir>/Matrix/
+ """
+ destdir = os.path.join(bustard_dir, 'Matrix')
+ if not os.path.isdir(destdir):
+ os.mkdir(destdir)
+
+ source = os.path.join(TESTDATA_DIR, '61MMFAAXX_4_1_matrix.txt')
+ for lane in LANE_LIST:
+ destination = os.path.join(destdir, 's_%d_1_matrix.txt' % ( lane, ))
+ shutil.copy(source, destination)
+
def make_phasing_dir(bustard_dir):
"""
Create several phasing files in <bustard_dir>/Phasing/
f.write(eland_multi[0])
f.close()
+def make_eland_export(gerald_dir, paired=False, lane_list=LANE_LIST):
+ source = os.path.join(TESTDATA_DIR, 'casava_1.7_export.txt')
+
+ for i in lane_list:
+ destination = os.path.join(gerald_dir,
+ 's_%d_export.txt' % (i,))
+ shutil.copy(source, destination)
+
+
def make_scarf(gerald_dir, lane_list=LANE_LIST):
seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
--- /dev/null
+#!/usr/bin/env python
+"""More direct synthetic test cases for the eland output file processing
+"""
+from StringIO import StringIO
+import unittest
+
+from htsworkflow.pipelines.eland import ElandLane
+
+class ElandTests(unittest.TestCase):
+ """Test specific Eland modules
+ """
+ def compare_match_array(self, current, expected):
+ for key in expected.keys():
+ self.failUnlessEqual(current[key], expected[key],
+ "Key %s: %s != %s" % (key,current[key],expected[key]))
+
+ def test_eland_score_mapped_mismatches(self):
+ eland = ElandLane()
+ match_codes = {'NM':0, 'QC':0, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ }
+ r = eland._score_mapped_mismatches("QC", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_QC)
+ self.compare_match_array(match_codes,
+ {'NM':0, 'QC':1, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ })
+
+ r = eland._score_mapped_mismatches("NM", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_QC)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ })
+
+ r = eland._score_mapped_mismatches("1:0:0", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_READ)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':1, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ })
+
+ r = eland._score_mapped_mismatches("2:4:16", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_READ)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':1, 'U1':0, 'U2':0,
+ 'R0':2, 'R1':4, 'R2':16,
+ })
+
+ r = eland._score_mapped_mismatches("1:1:1", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_READ)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':2, 'U1':1, 'U2':1,
+ 'R0':2, 'R1':4, 'R2':16,
+ })
+
+ r = eland._score_mapped_mismatches("1:0:0", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_READ)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':3, 'U1':1, 'U2':1,
+ 'R0':2, 'R1':4, 'R2':16,
+ })
+
+ r = eland._score_mapped_mismatches("0:0:1", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_READ)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':3, 'U1':1, 'U2':2,
+ 'R0':2, 'R1':4, 'R2':16,
+ })
+
+ r = eland._score_mapped_mismatches("chr3.fa", match_codes)
+ self.failUnlessEqual(r, ElandLane.SCORE_UNRECOGNIZED)
+ self.compare_match_array(match_codes,
+ {'NM':1, 'QC':1, 'RM':0,
+ 'U0':3, 'U1':1, 'U2':2,
+ 'R0':2, 'R1':4, 'R2':16,
+ })
+
+ def test_count_mapped_export(self):
+ eland = ElandLane()
+ mapped_reads = {}
+ r = eland._count_mapped_export(mapped_reads, "chr3.fa", "38")
+ self.failUnlessEqual(mapped_reads['chr3.fa'], 1)
+ self.failUnlessEqual(r, 'U0')
+
+ mapped_reads = {}
+ r = eland._count_mapped_export(mapped_reads, "chr3.fa", "36A4")
+ self.failUnlessEqual(mapped_reads['chr3.fa'], 1)
+ self.failUnlessEqual(r, 'U1')
+
+ mapped_reads = {}
+ r = eland._count_mapped_export(mapped_reads, "chr3.fa", "30A2T2")
+ self.failUnlessEqual(mapped_reads['chr3.fa'], 1)
+ self.failUnlessEqual(r, 'U2')
+
+ mapped_reads = {}
+ r = eland._count_mapped_export(mapped_reads, "chr3.fa", "26AG2T2")
+ self.failUnlessEqual(mapped_reads['chr3.fa'], 1)
+ self.failUnlessEqual(r, 'U2')
+
+ # deletion
+ mapped_reads = {}
+ r = eland._count_mapped_export(mapped_reads, "chr3.fa", "26^AG$4")
+ self.failUnlessEqual(mapped_reads['chr3.fa'], 1)
+ self.failUnlessEqual(r, 'U2')
+
+ # insertion
+ mapped_reads = {}
+ r = eland._count_mapped_export(mapped_reads, "chr3.fa", "26^2$4")
+ self.failUnlessEqual(mapped_reads['chr3.fa'], 1)
+ self.failUnlessEqual(r, 'U0')
+
+ def test_update_eland_export(self):
+ """Test scoring the pipeline export file"""
+ eland = ElandLane()
+ qc_read = StringIO("ILLUMINA-33A494 1 1 1 3291 1036 0 1 GANNTCCTCACCCGACANNNNNNNANNNCGGGNNACTC \XBB]^^^^[`````BBBBBBBBBBBBBBBBBBBBBBB QC")
+ one_read_exact = StringIO("ILLUMINA-33A494 1 1 1 2678 1045 0 1 AAGGTGAAGAAGGAGATGNNGATGATGACGACGATAGA ]]WW[[W]W]]R\WWZ[RBBS^\XVa____]W[]]___ chrX.fa 148341829 F 38 45")
+ one_read_mismatch = StringIO("ILLUMINA-33A494 1 1 1 2678 1045 0 1 AAGGTGAAGAAGGAGATGNNGATGATGACGACGATAGA ]]WW[[W]W]]R\WWZ[RBBS^\XVa____]W[]]___ chrX.fa 148341829 F 18AA15G1T 45")
+ multi_read = StringIO("ILLUMINA-33A494 1 1 1 4405 1046 0 1 GTGGTTTCGCTGGATAGTNNGTAGGGACAGTGGGAATC ``````````__a__V^XBB^SW^^a_____a______ 9:2:1")
+
+ match_codes, match_reads, reads = eland._update_eland_export(qc_read)
+ self.compare_match_array(match_codes,
+ {'NM':0, 'QC':1, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ })
+ self.failUnlessEqual(len(match_reads), 0)
+ self.failUnlessEqual(reads, 1)
+
+ match_codes, match_reads, reads = eland._update_eland_export(one_read_exact)
+ self.compare_match_array(match_codes,
+ {'NM':0, 'QC':0, 'RM':0,
+ 'U0':1, 'U1':0, 'U2':0,
+ 'R0':0, 'R1':0, 'R2':0,
+ })
+ self.failUnlessEqual(match_reads['chrX.fa'], 1)
+ self.failUnlessEqual(reads, 1)
+
+ match_codes, match_reads, reads = eland._update_eland_export(one_read_mismatch)
+ self.compare_match_array(match_codes,
+ {'NM':0, 'QC':0, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':1,
+ 'R0':0, 'R1':0, 'R2':0,
+ })
+ self.failUnlessEqual(match_reads['chrX.fa'], 1)
+ self.failUnlessEqual(reads, 1)
+
+ match_codes, match_reads, reads = eland._update_eland_export(multi_read)
+ self.compare_match_array(match_codes,
+ {'NM':0, 'QC':0, 'RM':0,
+ 'U0':0, 'U1':0, 'U2':1,
+ 'R0':9, 'R1':2, 'R2':0,
+ })
+ self.failUnlessEqual(len(match_reads), 0)
+ self.failUnlessEqual(reads, 1)
+
+
+def suite():
+ return unittest.makeSquite(ElandTests, 'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest="suite")
--- /dev/null
+#!/usr/bin/env python
+
+from datetime import datetime, date
+import os
+import tempfile
+import shutil
+import unittest
+
+from htsworkflow.pipelines import eland
+from htsworkflow.pipelines import ipar
+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,
+ '090608_HWI-EAS229_0117_4286GAAXX')
+ os.mkdir(runfolder_dir)
+
+ data_dir = os.path.join(runfolder_dir, 'Data')
+ os.mkdir(data_dir)
+
+ intensities_dir = make_rta_intensities_1870(data_dir)
+
+ basecalls_dir = make_rta_basecalls_1870(intensities_dir)
+ make_matrix_dir_rta160(basecalls_dir)
+
+ gerald_dir = os.path.join(basecalls_dir,
+ 'GERALD_07-09-2010_diane')
+ os.mkdir(gerald_dir)
+ make_gerald_config_100(gerald_dir)
+ make_summary_rta160_xml(gerald_dir)
+ make_eland_export(gerald_dir, lane_list=[1,2,3,4,5,6,])
+ make_scarf(gerald_dir, lane_list=[7,])
+ make_fastq(gerald_dir, lane_list=[8,])
+
+ if obj is not None:
+ obj.temp_dir = temp_dir
+ obj.runfolder_dir = runfolder_dir
+ obj.data_dir = data_dir
+ obj.image_analysis_dir = intensities_dir
+ obj.bustard_dir = basecalls_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_bustard(self):
+ """Construct a bustard object"""
+ b = bustard.bustard(self.bustard_dir)
+ self.failUnlessEqual(b.version, '1.8.70.0')
+ self.failUnlessEqual(b.date, None)
+ self.failUnlessEqual(b.user, None)
+ self.failUnlessEqual(len(b.phasing), 0)
+
+ 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)
+
+ 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 1.171 2008/05/19 17:36:14 mzerara Exp')
+ self.failUnlessEqual(g.date, datetime(2009,2,22,21,15,59))
+ 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/mm9',
+ '/g/mm9',
+ '/g/elegans190',
+ '/g/arabidopsis01222004',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9',
+ '/g/mm9', ]
+
+ # test lane specific parameters from gerald config file
+ for i in range(1,9):
+ cur_lane = g.lanes[i]
+ self.failUnlessEqual(cur_lane.analysis, 'eland_extended')
+ self.failUnlessEqual(cur_lane.eland_genome, genomes[i])
+ self.failUnlessEqual(cur_lane.read_length, '37')
+ self.failUnlessEqual(cur_lane.use_bases, 'Y'*37)
+
+ # I want to be able to use a simple iterator
+ for l in g.lanes.values():
+ self.failUnlessEqual(l.analysis, 'eland_extended')
+ self.failUnlessEqual(l.read_length, '37')
+ self.failUnlessEqual(l.use_bases, 'Y'*37)
+
+ # test data extracted from summary file
+ clusters = [None,
+ (281331, 11169), (203841, 13513),
+ (220889, 15653), (137294, 14666),
+ (129388, 14525), (262092, 10751),
+ (185754, 13503), (233765, 9537),]
+
+ self.failUnlessEqual(len(g.summary), 1)
+ for i in range(1,9):
+ summary_lane = g.summary[0][i]
+ self.failUnlessEqual(summary_lane.cluster, clusters[i])
+ self.failUnlessEqual(summary_lane.lane, 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)
+ return
+
+ # 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[i]
+ g2_lane = g2.lanes[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
+ self.failUnlessEqual(len(g.summary), 1)
+ for i in range(1,9):
+ g_summary = g.summary[0][i]
+ g2_summary = g2.summary[0][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.results[0].keys():
+ g_results = g_eland.results[0][lane]
+ g2_results = g2_eland.results[0][lane]
+ self.failUnlessEqual(g_results.reads,
+ g2_results.reads)
+ if isinstance(g_results, eland.ElandLane):
+ self.failUnlessEqual(len(g_results.mapped_reads),
+ len(g2_results.mapped_reads))
+ for k in g_results.mapped_reads.keys():
+ self.failUnlessEqual(g_results.mapped_reads[k],
+ g2_results.mapped_reads[k])
+
+ self.failUnlessEqual(len(g_results.match_codes),
+ len(g2_results.match_codes))
+ for k in g_results.match_codes.keys():
+ self.failUnlessEqual(g_results.match_codes[k],
+ g2_results.match_codes[k])
+
+
+ def test_eland(self):
+ return
+ 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_container = gerald.eland(self.gerald_dir, genome_maps=genome_maps)
+
+ # I added sequence lanes to the last 2 lanes of this test case
+ for i in range(1,7):
+ lane = eland_container.results[0][i]
+ self.failUnlessEqual(lane.reads, 6)
+ self.failUnlessEqual(lane.sample_name, "s")
+ self.failUnlessEqual(lane.lane_id, i)
+ self.failUnlessEqual(len(lane.mapped_reads), 17)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+ self.failUnlessEqual(lane.match_codes['U0'], 3)
+ 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)
+
+ # test scarf
+ lane = eland_container.results[0][7]
+ self.failUnlessEqual(lane.reads, 5)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 7)
+ self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
+
+ # test fastq
+ lane = eland_container.results[0][8]
+ self.failUnlessEqual(lane.reads, 3)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 8)
+ self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+
+ xml = eland_container.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_container.results[0][i]
+ l2 = e2.results[0][i]
+ self.failUnlessEqual(l1.reads, l2.reads)
+ self.failUnlessEqual(l1.sample_name, l2.sample_name)
+ self.failUnlessEqual(l1.lane_id, l2.lane_id)
+ if isinstance(l1, eland.ElandLane):
+ self.failUnlessEqual(len(l1.mapped_reads), len(l2.mapped_reads))
+ self.failUnlessEqual(len(l1.mapped_reads), 17)
+ 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])
+ elif isinstance(l1, eland.SequenceLane):
+ self.failUnlessEqual(l1.sequence_type, l2.sequence_type)
+
+ def test_runfolder(self):
+ return
+ runs = runfolder.get_runs(self.runfolder_dir)
+
+ # do we get the flowcell id from the filename?
+ self.failUnlessEqual(len(runs), 1)
+ name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ self.failUnlessEqual(runs[0].name, name)
+
+ # do we get the flowcell id from the FlowcellId.xml file
+ make_flowcell_id(self.runfolder_dir, '207BTAAXY')
+ runs = runfolder.get_runs(self.runfolder_dir)
+ self.failUnlessEqual(len(runs), 1)
+ name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+ 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")
+
--- /dev/null
+1.617195\r
+0.220814\r
+0\r
+0\r
+1.009254\r
+0.8633183\r
+0\r
+0\r
+0\r
+0\r
+1.319025\r
+0.05441951\r
+0\r
+0\r
+0.4378621\r
+0.676676\r
--- /dev/null
+ILLUMINA-33A494 1 1 1 2112 1040 0 1 CCNCATCTCAAAGAAGTNNNNNNNCNNNAAGTTTAATG \ZBZ^]]]]W__a_BBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 2130 1046 0 1 CTAGACCTGCAGGTGAGCNNGGTGGCCTATACATAGGC ^Z]PXG^^[Q^BBBBBBBBBBBBBBBBBBBBBBBBBBB 3:0:0 N
+ILLUMINA-33A494 1 1 1 2152 1043 0 1 CTTCCTCTTCACTCGGCCNNGANGGCNGCCGCCATAAG ^]]TU\[^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 2181 1040 0 1 CTNGGCTCTGGTATTTANNNNNNNTNNNTATTACATGG \LBSQ[T]XQY__BBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 2220 1045 0 1 GTGTTGTTGCCATGGTAANNCTGCTCAGTACGAGAGGA ``````````_____UXUBBX]YXX`T```____T___ 2:0:0 N
+ILLUMINA-33A494 1 1 1 2398 1045 0 1 CCACCAACTAAGCTTGGCNNTCCACCACCACCCACGGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NM N
+ILLUMINA-33A494 1 1 1 2468 1041 0 1 CTNCCTTTCTATGTGCCNNNNNNCTGNNAGGCCAGCCG ^^BZ\\]^]]____aBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 2537 1044 0 1 GACTCCCTCTCCATCGCCNNCGNGCCGCCTGGCCCATC ^H[^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 2678 1045 0 1 AAGGTGAAGAAGGAGATGNNGATGATGACGACGATAGA ]]WW[[W]W]]R\WWZ[RBBS^\XVa____]W[]]___ chrX.fa 148341829 F 18AA15G1T 45 N
+ILLUMINA-33A494 1 1 1 3023 1046 0 1 AGGCTCTGCCCAGCCCCGNNGAGGCCGCCGCCGCCGCC ```````````````[R^BBWZXPU_a___```````` chr7.fa 148513191 R 18AT18 117 N
+ILLUMINA-33A494 1 1 1 3042 1039 0 1 CCNGGCACTTGGGGTGGNNNNNNNGNNNGAGCNCAAGA \ZBZ^aaaa_`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3089 1043 0 1 GGACTCTCTTCTTCTTTTNNAANAGTNTTTTGATGCAC ```````````````]YYBB\]BZ[OBTX[^^\^]``` QC N
+ILLUMINA-33A494 1 1 1 3134 1041 0 1 ATNGTTCAGTAGATTTTNNNNNNAGANNCCATATTAGG ^^B^^^^]\[`````[[BBBBBBY\[BB][]^[Z^``` QC N
+ILLUMINA-33A494 1 1 1 3161 1041 0 1 TCNTAGCACCCACCATTGNNNNNAACNGCCACCACATT [YBTVZ\^Z[___^[\\UBBBBBRVOBVVVOUZRW___ QC N
+ILLUMINA-33A494 1 1 1 3186 1037 0 1 GGNNGGTTTAAAAAAAANNNNNNNANNNTTTGNNCAGT ]WBBVZRV[WW___BBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3291 1036 0 1 GANNTCCTCACCCGACANNNNNNNANNNCGGGNNACTC \XBB]^^^^[`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3338 1043 0 1 AGGGCGTATTGGTTCTTTNNNANATANTTTTATGGCGT `````_______a_aVROBBBZB[W[BUKOX^^W\a__ QC N
+ILLUMINA-33A494 1 1 1 3458 1037 0 1 GGNNGCTTGTTGGTGGANNNNNNNTNNNCTTCNNGGAC ]\BB][^^^[`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3577 1045 0 1 CCGCGTCCAACCCCAACCNNTGCTTGTTGTCATAAACT ```````````````^]^BB^^[^^````````````` chr2.fa 126187548 F 18GC18 117 N
+ILLUMINA-33A494 1 1 1 3615 1038 0 1 ATNNGATCCACTCTCTCNNNNNNNCNNNAAACNNAATC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3710 1045 0 1 CAAAGACCTTGTCATCGCNNGGTAACACAAGTCCCTTG ```````````````\ZZBB][TYV_________a___ chr19.fa 12878540 F 18AG18 117 N
+ILLUMINA-33A494 1 1 1 3751 1038 0 1 GANNGCAAATAAACAAANNNNNNNANNNGAAGNTGTTT ZUBBZ\]\^^`^^[`^^BBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3791 1038 0 1 CGNNTCTGCCCCTGTTGNNNNNNNGNNNGTCANNATTG [ZBBYZXWZ]`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3822 1037 0 1 GCNNATTATGGCCACGGNNNNNNNTNNNGGACNNTGTA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3842 1041 0 1 GGNCAGTGTGCATATTANNNNNNAGANNAAACTCCTCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 3997 1037 0 1 ATNNCAGTCATTCCCTANNNNNNNCNNNGATGNNAGAT VKBBZVOUV[WX___BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4021 1037 0 1 GGNNGCGGGTCGTGATGNNNNNNNANNNCAACNNTCCT [[BBSV[ZUS___aBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4071 1045 0 1 TGAGGGAAGAATGTTATGNNTACTCCTACGAATATGAT ```````````````[^^BB^^Z^X````````````` 2:1:0 N
+ILLUMINA-33A494 1 1 1 4107 1038 0 1 CGNCCGATTGGCGCCTCNNNNNNNCNNNTACANCAAAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4138 1036 0 1 AGNNTCACAGCTTGTTGNNNNNNNTNNNTGTTNNAGCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4349 1045 0 1 CTGTGAGCAGTAGTGGCTNNTGTTATGTCAACATAGGG aX__a___a_aa___ZZ\BBZV[YHUU[[\aX___X^^ chr6.fa 35461795 R 18GC18 116 N
+ILLUMINA-33A494 1 1 1 4372 1040 0 1 GANGTGTAGTAGGCAGANNNNNNNGNNNACTGGAGCTG ]LB]VZSP]P_____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4405 1046 0 1 GTGGTTTCGCTGGATAGTNNGTAGGGACAGTGGGAATC ``````````__a__V^XBB^SW^^a_____a______ 9:2:0 N
+ILLUMINA-33A494 1 1 1 4622 1040 0 1 GCNGGTACCAGACTTGCNNNNNNNTNNNTCCTCGTTAA \^B\Z^]]^^```W`BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4651 1038 0 1 AANAGAGTCATGACGGANNNNNNNCNNNAGCANTTTGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4674 1040 0 1 GANATCCGCCTGCCTCANNNNNNNGNNNGCTGGGATTA ^XB[^\]^[\`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4753 1040 0 1 CANTATTTGCTAACTCTNNNNNNNANNNCACCTCATCT ^^B\^^^^^^`````[[BBBBBBB^BBBY\[Z[^X``` QC N
+ILLUMINA-33A494 1 1 1 4826 1040 0 1 AGNGGCAGCAATAAGATNNNNNNNGNNNTTAAAAAGCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 4859 1045 0 1 CATTATTGTTATACCAAANNTCATATCCTATAATCTGG a_XX_[[__^`````^^^BB^\^SZ`````____a^__ Lambda_1-1_11936nts.fa 11716 F 18TG18 117 N
+ILLUMINA-33A494 1 1 1 4900 1043 0 1 AAAACCCCTTGTTTTATANNGANTTTNATCTTATTACC MU[OXUXMZZ^]^U^OOOBBWPBVWTBOVVZZ^Z^``` QC N
+ILLUMINA-33A494 1 1 1 5046 1046 0 1 AGTCGGTTGTAATGATACNNAACTCCAGGACACCAGTG ___a______````_Y[ZBB^^^^^````````````` chr10.fa 85365712 F CA16AG18 46 N
+ILLUMINA-33A494 1 1 1 5090 1040 0 1 CANACTGTAAGAGTCACNNNNNNNANNNCAATGCCTTT ^^B^^___aa`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5154 1038 0 1 ACNNGCATAGTTCACCANNNNNNNGNNNCTAANNCGTA YYBBVVYVTU__aaaBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5208 1037 0 1 TGNNTTTTTTTGTTTTGNNNNNNNTNNNTGGTNNCATT ]]BB\^^^^^^^BBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5268 1037 0 1 GTNNAGGGTGGGGGGCANNNNNNNTNNNATAGNNTCTC V]BBR[Y[Q[[^[^^BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5332 1038 0 1 GGNNGGGGGGCGGACGGNNNNNNNGNNNTGGANGGGGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5546 1044 0 1 CGCTGTGCTCTCGTCAGGNNATNCTGNGATTTGTTGGC ```````````````^]^BB\]B]\]B[[^]]^]^[`` QC N
+ILLUMINA-33A494 1 1 1 5603 1036 0 1 GGNNGAGCGATTTGTCTNNNNNNNTNNNATAANNAACN YOBB[LSOXOaaa__BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5710 1039 0 1 GCNGAATTAACCCATTGNNNNNNNCNNNTAGANTTTGG \\B\U\^\[\___aaBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5765 1043 0 1 CAGGGCGCCCGGGATCACNNGGNCTGNTAGGTCGATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5811 1045 0 1 GGGCTACTAAGGTGAACANNCGACTTCTTGTGAAGGGT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NM N
+ILLUMINA-33A494 1 1 1 5834 1037 0 1 CCNNGAGCATCTATGATNNNNNNNANNNTGATNNGCTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5865 1037 0 1 GGNNGGAGCCGCCGCAGNNNNNNNTNNNGGTGNNAGTA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 5892 1043 0 1 GTCGCTGTCTTTAGAGCTNNGCNTGCNTGCATGTCTTC ``````````_____^X^BB[ZBZ[]B[^[[^^\\``` QC N
+ILLUMINA-33A494 1 1 1 5939 1046 0 1 AAGACAGGATGTCTGTGTNNAATTGAACCTCTCTTGCC ```````````````][]BBZ\\Z]````````````` chr7.fa 75376418 F 18AA18 117 N
+ILLUMINA-33A494 1 1 1 5965 1041 0 1 TGNGTCCCACTGCAGAGNNNNNNGCCNNACCGGCCGCG ^^BXX[^[[X`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6000 1041 0 1 CTNTCTATTTTTTAATTNNNNNNTTTNNCCATGGCTGG ^TBV^\]T\\XX[[aWTBBBBBBV[RBB]]^^^[^``` QC N
+ILLUMINA-33A494 1 1 1 6083 1041 0 1 CTNAGATGGCCGGGGCTNNNNNNGCNNNACACTGACTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6416 1036 0 1 GCNNACTTCTTTTTCCANNNNNNNGNNNGATGNNTAAA \]BB\^^^^^`[^BBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6536 1036 0 1 GCNNGTATTTTATTTCTNNNNNNNCNNNAGGCNNTGAN ][BBV\LZ[[^T^BBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6641 1046 0 1 CATAAGGAAGTAGGTTTCNNAGAAACAGACCCCACTGG `````__I_____W_][[BBVYXYX`````````[[__ chr7.fa 148154014 F 18TG18 36 N
+ILLUMINA-33A494 1 1 1 6669 1037 0 1 GTNNACCTCTACATGCANNNNNNNCNNNCCCANNTCCC ]]BBY^X^^^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6707 1037 0 1 GGNNAGGGAAGGGAAGGNNNNNNNANNNAAGGNNAGGG [[BBR\\[NV_a___BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6936 1035 0 1 GCNNCTTATCCCTCAGCNNNNNNNGNNNACCCNNGGTN [VBB]^^^^^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 6973 1040 0 1 GTNCTGCAGTCCTCCCTNNNNNNNCNNNCCTGGGCAAC ^[B[^^][^[`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7024 1038 0 1 TGNNAGTGAGAGCCCACNNNNNNNCNNNAGGGNNAGCC ]\BBZ^W^X^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7062 1044 0 1 ACCTGCCTTTCTATGTGCNNTTNTGCNGCGAGGCCAGC aa____a_aa`````XZZBB\]B[ZZB\^^[]^][`_` QC N
+ILLUMINA-33A494 1 1 1 7151 1037 0 1 CGNNCCCGGTCATGACANNNNNNNGNNNACAGNNGACG [[BB[\[ZY]`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7444 1038 0 1 GCNNTTGTCTTGCTTAGNNNNNNNTNNNTTCCNNGTTA ]XBB]^^[[^___a_BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7491 1038 0 1 CTNNCCTTCAGTGACTGNNNNNNNGNNNCACCNNTGCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7520 1036 0 1 ATNNTGGCCAAATCTAANNNNNNNCNNNAGAANNGGCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7563 1044 0 1 GGAGAACCACCTGAACTTNNCANAGCNCGACGTCATCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7611 1041 0 1 AANAAGAAATCCTGCCTNNNNNNATANNAAGATGTATG YZBU[S[[XV_____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7672 1037 0 1 CCNNGCTGGGGTGGCATNNNNNNNTNNNATGTNNATCC []BBU^XVVV__[[^BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7702 1043 0 1 GGGTGCACAGGAGCTGGGNNNANCCANAGTGGCCACTC _______aXaa____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7728 1036 0 1 CCNNGCCATGAGTTTTTNNNNNNNCNNNTTCTNNTGGN ]]BBV^Z^XQ__a__BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 7849 1041 0 1 CTNCTCAGCATCACTACNNNNNNCTTNNGTCTTCCTCC ^\B^^\^^]]`````[ZBBBBBB^^[BB[ZZ[[X]``` QC N
+ILLUMINA-33A494 1 1 1 7919 1046 0 1 GTTCTGTTTTCCTTATTGNNGATGTGTTGTTGTTATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NM N
+ILLUMINA-33A494 1 1 1 8052 1037 0 1 GCNNTTAACTATGGGACNNNNNNNANNNAGTCNNACGT Y]BBW]UUU\_____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 8243 1042 0 1 GTNGTAATTCTCTGATTTNNNTNTTTNCTTGCTGGATT ^]B^\ZZ^^Z___a_\ZZBBB[B[[[BO]]^V\^^``` QC N
+ILLUMINA-33A494 1 1 1 8319 1036 0 1 GTNNATGTATTCCACTANNNNNNNANNNCTGTNNTCTT YZBBWYZ[Q[___X_BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 8400 1039 0 1 GCNGGGGGGTTCCGTGGNNNNNNNGNNNGTGTNTGTAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 8445 1038 0 1 GGNNCTGTAGGAAGGACNNNNNNNGNNNTACTNNGGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 8644 1038 0 1 CTNNGCAGTGACCTCATNNNNNNNGNNNCCCANNCCTA WSBBRZYX[R_a___BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 8662 1045 0 1 TGCCATTGTGAGGAACCTNNAGNGCATCATCTCCTAGG ]S]]S]T\^Xaa___[VVBBVWBXO\XMX\]^W][T^[ QC N
+ILLUMINA-33A494 1 1 1 8747 1044 0 1 AGAGGAAGCCCCCGACTCNNATNGAGNGGTGGATGGTG ```````````````^^[BBQYBZR[B[[P^[R^\___ QC N
+ILLUMINA-33A494 1 1 1 8831 1040 0 1 GGNGGAGGGAGGTCCAGNNNNNNNTNNNACATNTGTGT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9122 1039 0 1 GGNGATCCACTTAGTCCNNNNNNNGNNNGAGANAAAGG ][BUJW\XUZ____aBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9142 1039 0 1 CANAGATGTGTTTGGCTNNNNNNNCNNNACCANTTCAG ]\BXX[[^W^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9169 1045 0 1 GTTTTAAAGTTATTCCCTNNATNCTTTACTGAGACCTT _a____a_a_`````ZX^BBR[BSZ^^[]^```````` QC N
+ILLUMINA-33A494 1 1 1 9195 1036 0 1 GCNNCTTCTAAAGTATGNNNNNNNGNNNTTCGNNGGGN Y]BBW\W]Y[aa___BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9322 1040 0 1 GGNGTTTTAAATCTCCANNNNNNNANNNTACCNATATC ^]B^]^^^^]`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9393 1041 0 1 CANCACATTTATTTATCNNNNNNGTANNCTTACATCTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9520 1042 0 1 TTNCCCAGTTGCCAACTNNNNNNAGGNGACACGGTACC ^[B^^^^^\^`````^BBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9542 1044 0 1 CTGGTGGTGTACTATTCANNTGNTGANATCTGTACCAG a_________a__a_Z[]BBVWBVWNBUZZWZSZUa__ QC N
+ILLUMINA-33A494 1 1 1 9637 1040 0 1 AGNGCATGTCAAAGGACNNNNNNNTNNNCACANAGGTG YZB[FY[X[[___aaBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9731 1037 0 1 TCNNCTTGGAGTTTGAANNNNNNNTNNNGGAGNNCGAC ]]BBYZX\]X`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9760 1041 0 1 AGNCAGAACAACTCGCTNNNNNNCCTNNAGGGTATGCT \]B\YZ^]^^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9785 1038 0 1 GCNNTGGTCCAGCTGCANNNNNNNCNNNACTCNNGACC \]BBV^Z[^^`````^BBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9817 1036 0 1 TGNNCTTTCCTTTCAGGNNNNNNNGNNNAATCNNTTCN VWBBVOVVXY_____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 9888 1044 0 1 GCACATCCCAGGCTGACTNNGCNGTCNTGATTGTTGCT ```````````````\^[BB\\B\]^B^\U[[^][``` QC N
+ILLUMINA-33A494 1 1 1 9910 1037 0 1 GTNNTTTTAACTTGGTTNNNNNNNCNNNCTCCNNTAAA ]ZBB]\X[UY_aa_aBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 10024 1036 0 1 GGNNTGCATGGCTGGGCNNNNNNNCNNNAGCANNTTGN [\BB\\[^^[`````^BBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 10089 1038 0 1 CGNNAGTACTCTGTCAGNNNNNNNGNNNGCTCNNTTTC ]]BB]\\Z\^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 10220 1045 0 1 CTCTACTATTTCTACCTGNNCCNTCCTGGACTGTTGAA ```````````````^^]BB[]BX]^^^^\`````__a QC N
+ILLUMINA-33A494 1 1 1 10251 1044 0 1 ACCCCCTCTATTCGTCCCNNTCNTCTNGGAAATGCTAA ```````^^``````^^^BB]]B]\[B]Z[]^^^]``` QC N
+ILLUMINA-33A494 1 1 1 10567 1043 0 1 CTNGGCTTCTTGTGACCCNNNTNTTTNGCTTCCTTCCT ^^B^^^^\^^`````]^^BBB[BX[[B]\]_aaaa``` QC N
+ILLUMINA-33A494 1 1 1 10861 1043 0 1 GTNGGGTGATGATGAAACNNNTNCCANATTCTACCGCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
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+ILLUMINA-33A494 1 1 1 11038 1041 0 1 GTNGTGTGTGAGACTTTNNNNNNNGNNNTATTGAGGAC YUB]R[X^XZ[]H^^BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 11128 1041 0 1 CANGTACCGCCCTGATCNNNNNNNGNNNGCCATCCGCA ^[B^[^^^\]`[^``BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 11338 1039 0 1 GGNNACCAACACAATCTNNNNNNNTNNNTTCANNCTCC [YBB]ZZ^^Z`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 11402 1044 0 1 GGACCAGCCATAACATGCNNACNCCANTCGCCTCTGTA ```````````````^[[BBZUB[Z[B[\\\^][^___ QC N
+ILLUMINA-33A494 1 1 1 11626 1038 0 1 CTNNCGTAGCTCCCGGANNNNNNNGNNNGCCTNNGACA VSBBVZYYZY`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 11737 1039 0 1 ATNNGTTCCTTGGTTCTNNNNNNNCNNNCCCTNNTGTA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 11819 1038 0 1 ATNNGCGTTGCTGTGGTNNNNNNNGNNNACAANNAGCT ]QBB]\T[\X`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 11929 1046 0 1 GGGAATGCTATATCTGGGNNTCCGATTATTAGTGGGAC ```````````````^^^BB^]\^X``````````___ 2:0:0 N
+ILLUMINA-33A494 1 1 1 11981 1036 0 1 TTNNAATCAATGGGCTGNNNNNNNCNNNCTCANNGCTN ]]BB[Y][YV`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12039 1044 0 1 GTCACTTCTTACTCTAAGNNGGNGTCNCGCAGCTAGAG ```````````````^^^BB\]B[[XB[[[[^Y^[__a QC N
+ILLUMINA-33A494 1 1 1 12226 1037 0 1 CCNNTTTCACCCAACCGNNNNNNNTNNNGTGGNNCATG ]VBBY[YVVU`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12257 1045 0 1 GGCCTTAGCAACCAGGGTNNCCNTTCNTTCAATATTTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12291 1046 0 1 CCGAAGTGGAGAAGGGTTNNATGTGAACAGCAGTTGAA a____a_________^X^BBZ^ZX[_a_______aa__ 2:0:1 N
+ILLUMINA-33A494 1 1 1 12315 1043 0 1 GANATTTTGAAGAAAAAGNNNNNTGGNAGATACTAGTC ^WBW^^^^^[````[QUUBBBBBX]]BS]X][[^^``` QC N
+ILLUMINA-33A494 1 1 1 12339 1041 0 1 GANTAATCGAACCATCTNNNNNNNGNNNCCCTCCGAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12376 1037 0 1 ATNNTATATCTTGAAGANNNNNNNCNNNAGCANNGTTN BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12569 1038 0 1 CCNNCCTCAACAACCTCNNNNNNNCNNNTCCCNNCCAG ]WBBYZZUTZ`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12662 1040 0 1 GGNTAGCTTTGATGACANNNNNNNCNNNGAGTNCCTCC YYBVQXX\^Z_____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12850 1037 0 1 TGNNCCTTGCTTTTCTTNNNNNNNTNNNACTTNNGATC YYBBY\]\Y\`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12895 1039 0 1 GGNNTGTGTTTGGTCATNNNNNNNANNNATTTNNTAGA \^BB^^]^^[`````\^BBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 12949 1043 0 1 GGNGTTACGTGGAGGATGNNNGNGTGNCCTACATTTCC ^^B^^aaaa_`````I]]BBB[B[U^B^^^a_aa_``` QC N
+ILLUMINA-33A494 1 1 1 13225 1039 0 1 GTNNAAAAACTGGTGCANNNNNNNTNNNCGTTNNCCAG YXBBT[XVU[_____BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 13301 1035 0 1 CTNNGCAGGGCGAAGCCNNNNNNNANNNTGGTNNAGGN ]]BB][Z^^^`````^^BBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 13612 1047 0 1 AGGAGGACGAGGACACAGNNCTGGTAGACATGGCTTCG X`````````____aXZSBB[ZZZPX]]\]`````___ chr2.fa 13496052 R 18AC18 117 N
+ILLUMINA-33A494 1 1 1 13661 1041 0 1 CCNTGGCCCTAGTGACANNNNNNNCNNNAGAAGTTCTC ]VB]][^[[XaX__BBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 13705 1043 0 1 AGNGCAGCTCAGACAGAGNNNNNTCANCTGAGAGCTCT ^^B^^]^^]^`````^ZZBBBBBZ]ZB\]Z\][]Y``` QC N
+ILLUMINA-33A494 1 1 1 14048 1044 0 1 CCTGTGGATGTCATGCGGNNGGNCGGNATCAAAGTCAC ]]]Y]]US]]^BBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 14338 1036 0 1 GGNNAACCTCTTTCCATNNNNNNNGNNNACAANNGGGN BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 14371 1042 0 1 GGNTGGAAAAGGTTCCGNNNNNNTGNNNAGGGAGTAGT [ZBUY[[\[^_a_a_BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 14614 1037 0 1 CCNNAGCAGTTCGATTTNNNNNNNGNNNCCCANNTACA ^^BB^^^]^^`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 14633 1039 0 1 GANNGATAGTCAACAAGNNNNNNNANNNAAAGNNGAAA [ZBB]XX[^\`````BBBBBBBBBBBBBBBBBBBBBBB QC N
+ILLUMINA-33A494 1 1 1 14668 1042 0 1 AGNCCCTGATAGTTGGANNNNNNGATNCACTTGAGTAG ^^B^^][^[^`````\\BBBBBBYZ]B]]W^^\X[___ QC N
+ILLUMINA-33A494 1 1 1 14687 1045 0 1 GGAGAAGGAACTTACAAANNGTNTAGNAGATCAAAAAG aa_____a_a`````T[VBB]\BXWZB]]S^]Y]]``` QC N
--- /dev/null
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+ <Time />\r
+ <User />\r
+ </Run>\r
+</ImageAnalysis>
\ No newline at end of file
projects / htsworkflow.git / commitdiff