def sigproc(analysisArgs, pathtorawblock, SIGPROC_RESULTS):
printtime("RUNNING SINGLE BLOCK ANALYSIS")
command = "%s >> ReportLog.html 2>&1" % (analysisArgs)
printtime("Analysis command: " + command)
sys.stdout.flush()
sys.stderr.flush()
status = subprocess.call(command,shell=True)
blockprocessing.add_status("Analysis", status)
# write return code into file
try:
os.umask(0002)
f = open(os.path.join(SIGPROC_RESULTS,"analysis_return_code.txt"), 'w')
f.write(str(status))
f.close()
except:
traceback.print_exc()
if status == 2:
printtime("Analysis finished with status '%s'" % status)
try:
com = "ChkDat"
com += " -r %s" % (pathtorawblock)
# printtime("DEBUG: Calling '%s':" % com)
# ret = subprocess.call(com,shell=True)
except:
traceback.print_exc()
########################################################
#Make Bead Density Plots #
########################################################
printtime("Make Bead Density Plots")
bfmaskPath = os.path.join(SIGPROC_RESULTS,"analysis.bfmask.bin")
maskpath = os.path.join(SIGPROC_RESULTS,"MaskBead.mask")
if os.path.isfile(bfmaskPath):
com = "BeadmaskParse"
com += " -m MaskBead"
com += " %s" % bfmaskPath
ret = subprocess.call(com,shell=True)
blockprocessing.add_status("BeadmaskParse", ret)
try:
shutil.move('MaskBead.mask', maskpath)
except:
printtime("ERROR: MaskBead.mask already moved")
else:
printtime("Warning: no analysis.bfmask.bin file exists.")
if os.path.exists(maskpath):
try:
# Makes Bead_density_contour.png
beadDensityPlot.genHeatmap(maskpath, SIGPROC_RESULTS)
# os.remove(maskpath)
except:
traceback.print_exc()
else:
printtime("Warning: no MaskBead.mask file exists.")
printtime("Finished single block analysis")
def basecalling(
SIGPROC_RESULTS,
previousReport,
basecallerArgs,
libKey,
tfKey,
runID,
floworder,
reverse_primer_dict,
BASECALLER_RESULTS):
try:
if basecallerArgs:
cmd = basecallerArgs
else:
cmd = "BaseCaller"
if previousReport:
cmd += " --input-dir=%s" % (os.path.join(previousReport,SIGPROC_RESULTS))
else:
cmd += " --input-dir=%s" % (SIGPROC_RESULTS)
cmd += " --librarykey=%s" % (libKey)
cmd += " --tfkey=%s" % (tfKey)
cmd += " --run-id=%s" % (runID)
cmd += " --output-dir=%s" % (BASECALLER_RESULTS)
# 3' adapter details
qual_cutoff = reverse_primer_dict['qual_cutoff']
qual_window = reverse_primer_dict['qual_window']
adapter_cutoff = reverse_primer_dict['adapter_cutoff']
adapter = reverse_primer_dict['sequence']
cmd += " --flow-order %s" % (floworder)
cmd += " --trim-qual-cutoff %s" % (qual_cutoff)
cmd += " --trim-qual-window-size %s" % (qual_window)
cmd += " --trim-adapter-cutoff %s" % (adapter_cutoff)
cmd += " --trim-adapter %s" % (adapter)
cmd += " --trim-min-read-len 5"
cmd += " --bead-summary"
cmd += " >> ReportLog.html 2>&1"
printtime("DEBUG: Calling '%s':" % cmd)
ret = subprocess.call(cmd,shell=True)
blockprocessing.add_status("BaseCaller", ret)
except:
printtime('ERROR: BaseCaller failed')
traceback.print_exc()
def post_basecalling(
libsff_path,
reverse_primer_dict,
skipsfftrim,
sfftrim_args,
libKey,
floworder,
barcodeId,
barcodesplit_filter,
DIR_BC_FILES,
barcodeList_path,
bfmask_path,
barcodeMask_path,
generate_beadsummary,
BASECALLER_RESULTS):
if not os.path.exists(libsff_path):
printtime("ERROR: %s does not exist" % libsff_path)
open('badblock.txt', 'w').close()
return
##################################################
# Trim the SFF file if it has been requested #
##################################################
if not skipsfftrim:
printtime("Attempting to trim the SFF file")
libsff_untrimmed_path = libsff_path
(head,tail) = os.path.split(libsff_untrimmed_path)
libsff_trimmed_path = os.path.join(head,tail[:-4] + ".trimmed.sff")
try:
com = "SFFTrim"
com += " --in-sff %s" % (libsff_untrimmed_path)
com += " --out-sff %s" % (libsff_trimmed_path)
if sfftrim_args:
printtime("using non default args '%s'" % sfftrim_args)
com += " " + sfftrim_args
else:
printtime("no special args found, using default args")
# 3' adapter details
qual_cutoff = reverse_primer_dict['qual_cutoff']
qual_window = reverse_primer_dict['qual_window']
adapter_cutoff = reverse_primer_dict['adapter_cutoff']
adapter = reverse_primer_dict['sequence']
com += " --flow-order %s" % (floworder)
com += " --key %s" % (libKey)
com += " --qual-cutoff %s" % (qual_cutoff)
com += " --qual-window-size %s" % (qual_window)
com += " --adapter-cutoff %s" % (adapter_cutoff)
com += " --adapter %s" % (adapter)
com += " --min-read-len 5"
if generate_beadsummary:
com += " --bead-summary %s" % (os.path.join(BASECALLER_RESULTS, 'BaseCaller.json'))
printtime("DEBUG: Calling '%s':" % com)
ret = subprocess.call(com,shell=True)
blockprocessing.add_status("SFFTrim", ret)
except:
printtime('Failed SFFTrim')
traceback.print_exc()
if os.path.exists(libsff_untrimmed_path):
printtime ("DEBUG: remove untrimmed file %s" % libsff_untrimmed_path)
os.remove(libsff_untrimmed_path)
else:
printtime ("ERROR: untrimmed file not found: %s" % libsff_untrimmed_path)
if os.path.exists(libsff_trimmed_path):
printtime ("DEBUG: Renaming %s to %s" % (libsff_trimmed_path,libsff_path))
os.rename(libsff_trimmed_path,libsff_path)
else:
printtime("Not attempting to trim the SFF")
#####################################################
# Barcode trim SFF if barcodes have been specified #
# Creates one fastq per barcode, plus unknown reads #
#####################################################
if barcodeId != '':
try:
(head,tail) = os.path.split(libsff_path)
libsff_bctrimmed_path = os.path.join(head,tail[:-4] + ".bctrimmed.sff")
if not os.path.exists(DIR_BC_FILES):
os.mkdir(DIR_BC_FILES)
com = "barcodeSplit"
com += " -s"
com += " -i %s" % libsff_path
com += " -b %s" % barcodeList_path
com += " -k %s" % bfmask_path
com += " -f %s" % floworder
com += " -l %s" % barcodesplit_filter
com += " -c %s" % barcodeMask_path
com += " -d %s" % DIR_BC_FILES
printtime("DEBUG: Calling '%s'" % com)
ret = subprocess.call(com,shell=True)
blockprocessing.add_status("barcodeSplit", ret)
if int(ret) != 0:
printtime("ERROR Failed barcodeSplit with return code %d" % int(ret))
else:
# barcodeSplit is producing "bctrimmed_"+libsff_path , rename
(head,tail) = os.path.split(libsff_path)
bcsff = os.path.join(DIR_BC_FILES,head,"bctrimmed_"+tail)
if os.path.exists(bcsff):
printtime ("Renaming %s to %s" % (bcsff, libsff_bctrimmed_path))
os.rename(bcsff,libsff_bctrimmed_path)
else:
printtime ("ERROR: Renaming: File not found: %s" % bcsff)
if os.path.exists(libsff_path):
printtime ("DEBUG: remove file %s" % libsff_path)
os.remove(libsff_path)
else:
printtime ("ERROR: Remove: File not found: %s" % libsff_path)
#rename: libsff_path contains now the trimmed/bctrimmed data
if os.path.exists(libsff_bctrimmed_path):
printtime ("Renaming %s to %s" % (libsff_bctrimmed_path,libsff_path))
os.rename(libsff_bctrimmed_path,libsff_path)
except:
printtime("ERROR Failed barcodeSplit")
traceback.print_exc()
# implement barcode filtering by moving filtered files
if float(barcodesplit_filter) > 0:
from ion.utils.filter_barcodes import filter_barcodes
filter_barcodes(DIR_BC_FILES)
##################################################
# Once we have the new SFF, run SFFSummary
# to get the predicted quality scores
##################################################
try:
com = "SFFSummary"
com += " -o %s" % os.path.join(BASECALLER_RESULTS, 'quality.summary')
com += " --sff-file %s" % libsff_path
com += " --read-length 50,100,150"
com += " --min-length 0,0,0"
com += " --qual 0,17,20"
com += " -d %s" % os.path.join(BASECALLER_RESULTS, 'readLen.txt')
printtime("DEBUG: Calling '%s'" % com)
ret = subprocess.call(com,shell=True)
blockprocessing.add_status("SFFSummary", ret)
except:
printtime('Failed SFFSummary')
printtime("make the read length histogram")
try:
filepath_readLenHistogram = os.path.join(BASECALLER_RESULTS,'readLenHisto.png')
trimmedReadLenHisto.trimmedReadLenHisto('readLen.txt',filepath_readLenHistogram)
except:
printtime("Failed to create %s" % filepath_readLenHistogram)
#####################################################
# make keypass.fastq file -c(cut key) -k(key flows) #
#####################################################
try:
com = "SFFRead"
com += " -q %s" % libsff_path.replace(".sff",".fastq")
com += " %s" % libsff_path
com += " > %s" % os.path.join(BASECALLER_RESULTS, 'keypass.summary')
printtime("DEBUG: Calling '%s'" % com)
ret = subprocess.call(com,shell=True)
blockprocessing.add_status("SFFRead", ret)
except:
printtime('Failed SFFRead')
printtime('Failed to convert SFF ' + str(libsff_path) + ' to fastq')
def alignment_unmapped_bam(
BASECALLER_RESULTS,
ALIGNMENT_RESULTS,
align_full,
libraryName,
flows,
aligner_opts_extra,
mark_duplicates,
bidirectional,
sam_parsed):
printtime("Attempt to align")
datasets_basecaller_path = os.path.join(BASECALLER_RESULTS,"datasets_basecaller.json")
if not os.path.exists(datasets_basecaller_path):
printtime("ERROR: %s does not exist" % datasets_basecaller_path)
open('badblock.txt', 'w').close()
return
datasets_basecaller = {}
try:
f = open(datasets_basecaller_path,'r')
datasets_basecaller = json.load(f);
f.close()
except:
printtime("ERROR: problem parsing %s" % datasets_basecaller_path)
traceback.print_exc()
open('badblock.txt', 'w').close()
return
# establish the read-length histogram range by using the simple rule:
# 0.7 * num_flows rounded up to a next multiple of 50
try:
graph_max_x = int(50 * math.ceil(0.014 * int(flows)))
except:
graph_max_x = 400
input_prefix_list = []
for dataset in datasets_basecaller["datasets"]:
if not os.path.exists(os.path.join(BASECALLER_RESULTS, dataset['basecaller_bam'])):
continue
#-----------------------------------
# DEFAULT SINGLE SFF/FASTQ BEHAVIOR - (Runs for barcoded runs too)
#-----------------------------------
try:
com = "alignmentQC.pl"
if align_full:
com += " --align-all-reads"
com += " --logfile %s" % os.path.join(ALIGNMENT_RESULTS,dataset['file_prefix']+'.alignmentQC_out.txt')
com += " --output-dir %s" % ALIGNMENT_RESULTS
com += " --out-base-name %s" % dataset['file_prefix']
com += " --input %s" % os.path.join(BASECALLER_RESULTS, dataset['basecaller_bam'])
com += " --genome %s" % libraryName
#com += " --max-plot-read-len %s" % str(int(graph_max_x))
com += " --max-plot-read-len %s" % str(int(400))
if sam_parsed:
com += ' -p 1'
if bidirectional:
com += ' --bidirectional'
if aligner_opts_extra:
com += ' --aligner-opts-extra "%s"' % aligner_opts_extra
if mark_duplicates:
com += ' --mark-duplicates'
com += " >> %s 2>&1" % os.path.join(ALIGNMENT_RESULTS, 'alignment.log')
printtime("Alignment QC command line:\n%s" % com)
retcode = subprocess.call(com, shell=True)
blockprocessing.add_status("alignmentQC.pl", retcode)
if retcode != 0:
printtime("alignmentQC failed, return code: %d" % retcode)
alignError = open("alignment.error", "w")
alignError.write(com)
alignError.write('alignmentQC returned with error code: ')
alignError.write(str(retcode))
alignError.close()
except OSError:
printtime('ERROR: Alignment Failed to start')
alignError = open("alignment.error", "w")
alignError.write(str(traceback.format_exc()))
alignError.close()
traceback.print_exc()
printtime("Barcode processing, rename")
if os.path.exists(os.path.join(ALIGNMENT_RESULTS,'alignment.summary')):
try:
fname=os.path.join(ALIGNMENT_RESULTS,dataset['file_prefix']+'.alignment.summary')
os.rename(os.path.join(ALIGNMENT_RESULTS,'alignment.summary'), fname)
fname=os.path.join(ALIGNMENT_RESULTS,dataset['file_prefix']+'.alignTable.txt')
os.rename(os.path.join(ALIGNMENT_RESULTS,'alignStats_err.txt'), fname)
except:
printtime('error renaming')
traceback.print_exc()
alignment_post_processing(BASECALLER_RESULTS, ALIGNMENT_RESULTS, flows, mark_duplicates, False)
printtime("**** Alignment completed ****")
def align_full_chip(
SAM_META,
libsff_path,
align_full,
graph_max_x,
make_align_graphs,
sam_parsed,
bidirectional,
libraryName,
flows,
opts_extra,
mark_duplicates,
outputdir,
outBaseName=''
):
printtime("sam_parsed is %s" % sam_parsed)
#Now build the SAM meta data arg string
aligner_opts_rg= '--aligner-opts-rg "'
aligner_opts_extra = ''
additional_aligner_opts = ''
if sam_parsed:
additional_aligner_opts += ' -p 1'
if bidirectional:
additional_aligner_opts += ' --bidirectional'
if opts_extra:
print ' found extra alignment options: "%s"' % opts_extra
aligner_opts_extra = ' --aligner-opts-extra "'
aligner_opts_extra += opts_extra + '"'
first = True
for key, value in SAM_META.items():
if value:
sam_arg = r'-R \"'
end = r'\"'
sam_arg = sam_arg + key + ":" + value + end
if first:
aligner_opts_rg = aligner_opts_rg + sam_arg
first = False
else:
aligner_opts_rg = aligner_opts_rg + " " + sam_arg
#add the trailing quote
aligner_opts_rg = aligner_opts_rg + '"'
if 0 < graph_max_x:
# establish the read-length histogram range by using the simple rule: 0.6 * num-flows
flowsUsed = 0
try:
flowsUsed = int(flows)
except:
flowsUsed = 400
graph_max_x = 100 * math.trunc((0.6 * flowsUsed + 99)/100.0)
if graph_max_x < 400:
graph_max_x = 400
#-----------------------------------
# DEFAULT SINGLE SFF/FASTQ BEHAVIOR - (Runs for barcoded runs too)
#-----------------------------------
try:
com = "alignmentQC.pl"
if (align_full):
com += " --align-all-reads"
com += " --logfile %s" % os.path.join(outputdir,"alignmentQC_out.txt")
com += " --output-dir %s" % outputdir
com += " --input %s" % libsff_path
com += " --genome %s" % libraryName
com += " --max-plot-read-len %s" % graph_max_x
if len(outBaseName) > 1:
com += " --out-base-name %s" % outBaseName
else:
com += " %s" % (additional_aligner_opts)
com += " %s %s" % (aligner_opts_rg,aligner_opts_extra)
if mark_duplicates:
com += " --mark-duplicates"
com += " >> %s 2>&1" % os.path.join(outputdir, 'alignment.log')
printtime("Alignment QC command line:\n%s" % com)
retcode = subprocess.call(com, shell=True)
blockprocessing.add_status("alignmentQC.pl", retcode)
if retcode != 0:
printtime("alignmentQC failed, return code: %d" % retcode)
alignError = open("alignment.error", "w")
alignError.write(com)
alignError.write('alignmentQC returned with error code: ')
alignError.write(str(retcode))
alignError.close()
except OSError:
printtime('ERROR: Alignment Failed to start')
alignError = open("alignment.error", "w")
alignError.write(str(traceback.format_exc()))
alignError.close()
traceback.print_exc()
if make_align_graphs:
makeAlignGraphs()
def align_full_chip(
SAM_META,
libsff_path,
align_full,
graph_max_x,
do_barcode,
make_align_graphs,
sam_parsed,
bidirectional,
DIR_BC_FILES,
libraryName,
flows,
barcodeId,
opts_extra,
outputdir):
printtime("sam_parsed is %s" % sam_parsed)
#Now build the SAM meta data arg string
aligner_opts_rg= '--aligner-opts-rg "'
aligner_opts_extra = ''
additional_aligner_opts = ''
if sam_parsed:
additional_aligner_opts += ' -p 1'
if bidirectional:
additional_aligner_opts += ' --bidirectional'
if opts_extra:
print ' found extra alignment options: "%s"' % opts_extra
aligner_opts_extra = ' --aligner-opts-extra "'
aligner_opts_extra += opts_extra + '"'
first = True
for key, value in SAM_META.items():
if value:
sam_arg = r'-R \"'
end = r'\"'
sam_arg = sam_arg + key + ":" + value + end
if first:
aligner_opts_rg = aligner_opts_rg + sam_arg
first = False
else:
aligner_opts_rg = aligner_opts_rg + " " + sam_arg
#add the trailing quote
aligner_opts_rg = aligner_opts_rg + '"'
if 0 < graph_max_x:
# establish the read-length histogram range by using the simple rule: 0.6 * num-flows
flowsUsed = 0
try:
flowsUsed = int(flows)
except:
flowsUsed = 400
graph_max_x = 100 * math.trunc((0.6 * flowsUsed + 99)/100.0)
if graph_max_x < 400:
graph_max_x = 400
#-----------------------------------
# DEFAULT SINGLE SFF/FASTQ BEHAVIOR - (Runs for barcoded runs too)
#-----------------------------------
if (align_full):
#If a full align is forced add a '--align-all-reads' flag
com = "alignmentQC.pl"
com += " --logfile %s" % os.path.join(outputdir,"alignmentQC_out.txt")
com += " --output-dir %s" % outputdir
com += " --input %s" % libsff_path
com += " --genome %s" % libraryName
com += " --max-plot-read-len %s" % graph_max_x
com += " --align-all-reads"
com += " %s" % (additional_aligner_opts)
com += " %s %s" % (aligner_opts_rg,aligner_opts_extra)
com += " >> ReportLog.html 2>&1"
else:
com = "alignmentQC.pl"
com += " --logfile %s" % os.path.join(outputdir,"alignmentQC_out.txt")
com += " --output-dir %s" % outputdir
com += " --input %s" % libsff_path
com += " --genome %s" % libraryName
com += " --max-plot-read-len %s" % graph_max_x
com += " %s" % (additional_aligner_opts)
com += " %s %s" % (aligner_opts_rg,aligner_opts_extra)
com += " >> ReportLog.html 2>&1"
try:
printtime("Alignment QC command line:\n%s" % com)
retcode = subprocess.call(com, shell=True)
blockprocessing.add_status("alignmentQC.pl", retcode)
if retcode != 0:
printtime("alignmentQC failed, return code: %d" % retcode)
alignError = open("alignment.error", "w")
alignError.write('alignmentQC returned with error code: ')
alignError.write(str(retcode))
alignError.close()
except OSError:
printtime('Alignment Failed to start')
alignError = open("alignment.error", "w")
alignError.write(str(traceback.format_exc()))
alignError.close()
traceback.print_exc()
if make_align_graphs:
makeAlignGraphs()
#--------------------------------------------
# BARCODE HANDLING BEHAVIOR (Multiple FASTQ)
#--------------------------------------------
if barcodeId and do_barcode:
printtime("Renaming non-barcoded alignment results to 'comprehensive'")
files = [ 'alignment.summary',
'alignmentQC_out.txt',
'alignTable.txt',
]
for fname in files:
try:
#if os.path.exists(fname):
# os.rename(fname, fname + ".comprehensive")
shutil.copyfile(fname, fname + ".comprehensive")
except:
printtime('ERROR copying %s' % fname)
traceback.print_exc()
printtime("STARTING BARCODE ALIGNMENTS")
barcodelist_path = 'barcodeList.txt'
if not os.path.exists(barcodelist_path):
barcodelist_path = '../barcodeList.txt'
if not os.path.exists(barcodelist_path):
barcodelist_path = '../../barcodeList.txt'
if not os.path.exists(barcodelist_path):
printtime('ERROR: barcodeList.txt not found')
barcodeList = parse_bcfile(barcodelist_path)
align_full = True
top_dir = os.getcwd()
try:
os.chdir(DIR_BC_FILES)
printtime('DEBUG changing to %s for barcodes alignment' % DIR_BC_FILES)
except:
printtime('ERROR missing %s folder' % DIR_BC_FILES)
for bcid in (x['id_str'] for x in barcodeList):
(head,tail) = os.path.split(libsff_path)
sffName = os.path.join(head,"%s_%s" % (bcid, tail))
if os.path.exists(sffName):
printtime("Barcode processing for '%s': %s" % (bcid, sffName))
else:
printtime("No barcode SFF file found for '%s': %s" % (bcid, sffName))
continue
if (align_full):
printtime("Align All Reads")
#If a full align is forced add a '--align-all-reads' flag
com = "alignmentQC.pl"
com += " --logfile %s" % os.path.join(outputdir,"alignmentQC_out.txt")
com += " --output-dir %s" % outputdir
com += " --input %s" % sffName
com += " --genome %s" % libraryName
com += " --max-plot-read-len %s" % graph_max_x
com += " --align-all-reads"
com += " %s" % (additional_aligner_opts)
com += " %s %s" % (aligner_opts_rg, aligner_opts_extra)
com += " >> ReportLog.html 2>&1"
else:
printtime("Align Subset of Reads")
com = "alignmentQC.pl"
com += " --logfile %s" % os.path.join(outputdir,"alignmentQC_out.txt")
com += " --output-dir %s" % outputdir
com += " --input %s" % sffName
com += " --genome %s" % libraryName
com += " --max-plot-read-len %s" % graph_max_x
com += " %s" % (additional_aligner_opts)
com += " %s %s" % (aligner_opts_rg, aligner_opts_extra)
com += " >> ReportLog.html 2>&1"
try:
printtime("Alignment QC command line:\n%s" % com)
retcode = subprocess.call(com, shell=True)
blockprocessing.add_status("alignmentQC.pl", retcode)
if retcode != 0:
printtime("alignmentQC failed, return code: %d" % retcode)
alignError = open("alignment.error", "a")
alignError.write(com)
alignError.write(': \nalignmentQC returned with error code: ')
alignError.write(str(retcode))
alignError.close()
except:
printtime('ERROR: Alignment Failed to start')
alignError = open("alignment.error", "a")
alignError.write(str(traceback.format_exc()))
alignError.close()
traceback.print_exc()
#rename each output file based on barcode found in fastq filename
#but ignore the comprehensive fastq output files
if os.path.exists('alignment.summary'):
try:
fname='alignment_%s.summary' % bcid
os.rename('alignment.summary', fname)
# os.rename(fname,os.path.join(DIR_BC_FILES,fname))
fname='alignmentQC_out_%s.txt' % bcid
os.rename('alignmentQC_out.txt', fname)
# os.rename(fname,os.path.join(DIR_BC_FILES,fname))
fname='alignTable_%s.txt' % bcid
os.rename('alignTable.txt', fname)
# os.rename(fname,os.path.join(DIR_BC_FILES,fname))
except:
printtime('error renaming')
traceback.print_exc()
os.chdir(top_dir)
#rename comprehensive results back to default names
for fname in files:
#if os.path.exists(fname + '.comprehensive'):
# os.rename(fname + '.comprehensive', fname)
try:
shutil.copyfile(fname + '.comprehensive', fname)
except:
printtime('ERROR copying %s' % fname + '.comprehensive')
traceback.print_exc()
aggregate_alignment (DIR_BC_FILES,barcodelist_path)
def sigproc(analysisArgs, libKey, tfKey, pathtorawblock, SIGPROC_RESULTS, plot_title, oninstrumentanalysis):
printtime("RUNNING SINGLE BLOCK ANALYSIS")
if not oninstrumentanalysis:
if analysisArgs:
cmd = analysisArgs # e.g /home/user/Analysis --flowlimit 80
else:
cmd = "Analysis"
printtime("ERROR: Analysis command not specified, using default: 'Analysis'")
sigproc_log_path = os.path.join(SIGPROC_RESULTS, 'sigproc.log')
open(sigproc_log_path, 'w').close()
sigproc_log = open(sigproc_log_path)
cmd += " --librarykey=%s" % (libKey)
cmd += " --tfkey=%s" % (tfKey)
cmd += " --no-subdir"
cmd += " --output-dir=%s" % (SIGPROC_RESULTS)
cmd += " %s" % pathtorawblock
cmd += " >> %s 2>&1" % sigproc_log_path
printtime("Analysis command: " + cmd)
proc = subprocess.Popen(cmd, shell=True)
while proc.poll() is None:
where = sigproc_log.tell()
lines = sigproc_log.readlines()
if lines:
if any(l.startswith("Beadfind Complete") for l in lines):
printtime("Beadfind is complete.")
bfmaskPath = os.path.join(SIGPROC_RESULTS,"bfmask.bin")
bfmaskstatspath = os.path.join(SIGPROC_RESULTS,"bfmask.stats")
update_bfmask_artifacts(bfmaskPath, bfmaskstatspath, SIGPROC_RESULTS, plot_title)
else:
sigproc_log.seek(where)
time.sleep(1)
sigproc_log.close()
status = proc.wait()
blockprocessing.add_status("Analysis", status)
# write return code into file
try:
os.umask(0002)
f = open(os.path.join(SIGPROC_RESULTS,"analysis_return_code.txt"), 'w')
f.write(str(status))
f.close()
except:
traceback.print_exc()
if status == 2:
printtime("Analysis finished with status '%s'" % status)
try:
com = "ChkDat"
com += " -r %s" % (pathtorawblock)
# printtime("DEBUG: Calling '%s':" % com)
# ret = subprocess.call(com,shell=True)
except:
traceback.print_exc()
########################################################
#Make Bead Density Plots #
########################################################
bfmaskPath = os.path.join(SIGPROC_RESULTS,"analysis.bfmask.bin")
bfmaskstatspath = os.path.join(SIGPROC_RESULTS,"analysis.bfmask.stats")
update_bfmask_artifacts(bfmaskPath, bfmaskstatspath, SIGPROC_RESULTS, plot_title)
printtime("Finished single block analysis")
