def run_target_list_compilation(pInteractionFilesList,
pTargetList,
pArgs,
pViewpointObj,
pQueue=None):
outfile_names = []
target_regions_intervaltree = None
if pArgs.batchMode and len(pTargetList) == 1:
target_regions = utilities.readBed(pTargetList[0])
hicmatrix = hm.hiCMatrix()
target_regions_intervaltree = hicmatrix.intervalListToIntervalTree(
target_regions)[0]
for i, interactionFile in enumerate(pInteractionFilesList):
for sample in interactionFile:
if pArgs.interactionFileFolder != '.':
absolute_sample_path = pArgs.interactionFileFolder + '/' + sample
else:
absolute_sample_path = sample
header, interaction_data, interaction_file_data = pViewpointObj.readInteractionFileForAggregateStatistics(
absolute_sample_path)
log.debug('len(pTargetList) {}'.format(len(pTargetList)))
if pArgs.batchMode and len(pTargetList) > 1:
if pArgs.targetFileFolder != '.':
target_file = pArgs.targetFileFolder + '/' + pTargetList[i]
else:
target_file = pTargetList[i]
elif pArgs.batchMode and len(pTargetList) == 1:
target_file = None
else:
target_file = pTargetList[i]
accepted_scores = filter_scores_target_list(
interaction_file_data,
pTargetList=target_file,
pTargetIntervalTree=target_regions_intervaltree)
if len(accepted_scores) == 0:
# do not call 'break' or 'continue'
# with this an empty file is written and no track of 'no significant interactions' detected files needs to be recorded.
if pArgs.batchMode:
with open('errorLog.txt', 'a+') as errorlog:
errorlog.write('Failed for: {} and {}.\n'.format(
interactionFile[0], interactionFile[1]))
else:
log.info('No target regions found')
outFileName = '.'.join(sample.split('/')[-1].split('.')
[:-1]) + '_' + pArgs.outFileNameSuffix
if pArgs.batchMode:
outfile_names.append(outFileName)
if pArgs.outputFolder != '.':
outFileName = pArgs.outputFolder + '/' + outFileName
write(outFileName, header, accepted_scores, interaction_file_data)
if pQueue is None:
return
pQueue.put(outfile_names)
return
def filter_scores_target_list(pScoresDictionary,
pTargetList=None,
pTargetIntervalTree=None):
accepted_scores = {}
same_target_dict = {}
target_regions_intervaltree = None
if pTargetList is not None:
target_regions = utilities.readBed(pTargetList)
if len(target_regions) == 0:
return accepted_scores
hicmatrix = hm.hiCMatrix()
target_regions_intervaltree = hicmatrix.intervalListToIntervalTree(
target_regions)[0]
elif pTargetIntervalTree is not None:
target_regions_intervaltree = pTargetIntervalTree
else:
log.error('No target list given.')
exit(1)
for key in pScoresDictionary:
# try:
chromosome = pScoresDictionary[key][0]
start = int(pScoresDictionary[key][1])
end = int(pScoresDictionary[key][2])
if chromosome in target_regions_intervaltree:
target_interval = target_regions_intervaltree[chromosome][
start:end]
else:
continue
if target_interval:
target_interval = sorted(target_interval)[0]
if target_interval in same_target_dict:
same_target_dict[target_interval].append(key)
else:
same_target_dict[target_interval] = [key]
for target in same_target_dict:
values = np.array([0.0, 0.0, 0.0])
same_target_dict[target] = sorted(same_target_dict[target])
for key in same_target_dict[target]:
values += np.array(list(map(float, pScoresDictionary[key][-3:])))
new_data_line = pScoresDictionary[same_target_dict[target][0]]
new_data_line[2] = pScoresDictionary[same_target_dict[target][-1]][2]
new_data_line[-5] = pScoresDictionary[same_target_dict[target][-1]][-5]
new_data_line[-3] = values[0]
new_data_line[-2] = values[1]
new_data_line[-1] = values[2]
accepted_scores[same_target_dict[target][0]] = new_data_line
return accepted_scores
def run_target_list_compilation(pInteractionFilesList,
pTargetList,
pArgs,
pViewpointObj,
pQueue=None,
pOneTarget=False):
outfile_names_list = []
accepted_scores_list = []
target_regions_intervaltree = None
try:
if pOneTarget == True:
try:
target_regions = utilities.readBed(pTargetList)
except Exception as exp:
pQueue.put('Fail: ' + str(exp) + traceback.format_exc())
return
hicmatrix = hm.hiCMatrix()
target_regions_intervaltree = hicmatrix.intervalListToIntervalTree(
target_regions)[0]
for i, interactionFile in enumerate(pInteractionFilesList):
outfile_names_list_intern = []
accepted_scores_list_intern = []
for sample in interactionFile:
interaction_data, interaction_file_data, _ = pViewpointObj.readInteractionFile(
pArgs.interactionFile, sample)
if pOneTarget == True:
target_file = None
else:
target_file = pTargetList[i]
accepted_scores = filter_scores_target_list(
interaction_file_data,
pTargetList=target_file,
pTargetIntervalTree=target_regions_intervaltree,
pTargetFile=pArgs.targetFile)
outfile_names_list_intern.append(sample)
accepted_scores_list_intern.append(accepted_scores)
outfile_names_list.append(outfile_names_list_intern)
accepted_scores_list.append(accepted_scores_list_intern)
except Exception as exp:
pQueue.put('Fail: ' + str(exp) + traceback.format_exc())
return
if pQueue is None:
return
counter = 0
for item in accepted_scores_list_intern:
if len(item) == 0:
counter += 1
pQueue.put([outfile_names_list, accepted_scores_list])
return