def get_analysis_info(json_paths, sample_set_id):
'''Return the information in the analysis files for the given patient
under the provided json paths.
'''
analysis_file = get_analysis_from_sample_set(sample_set_id)
results = []
for analysis in analysis_file:
filename=defs.DIR_RESULTS + analysis.analysis_file
results.append(vidjil_utils.extract_fields_from_json(json_paths, None, filename))
return results
def get_analysis_info(json_paths, sample_set_id):
"""Return the information in the analysis files for the given patient
under the provided json paths.
"""
analysis_file = get_analysis_from_sample_set(sample_set_id)
results = []
for analysis in analysis_file:
filename = defs.DIR_RESULTS + analysis.analysis_file
results.append(vidjil_utils.extract_fields_from_json(json_paths, None, filename))
return results
def stats():
start = time.time()
d = custom()
stats_regex = [
# found 771265 40-windows in 2620561 segments (85.4%) inside 3068713 sequences # before 1f501e13 (-> 2015.05)
'in (?P<seg>\d+) segments \((?P<seg_ratio>.*?)\) inside (?P<reads>\d+) sequences',
# found 10750 50-windows in 13139 reads (99.9% of 13153 reads)
'windows in (?P<seg>\d+) reads \((?P<seg_ratio>.*?) of (?P<reads>\d+) reads\)',
# segmentation causes
'log.* SEG_[+].*?-> (?P<SEG_plus>.*?).n',
'log.* SEG_[-].*?-> (?P<SEG_minus>.*?).n',
]
# stats by locus
for locus in defs.LOCUS:
locus_regex = locus.replace('+', '[+]')
locus_group = locus.replace('+', 'p')
stats_regex += [
'log.* %(locus)s.*?->\s*?(?P<%(locus_g)s_reads>\d+)\s+(?P<%(locus_g)s_av_len>[0-9.]+)\s+(?P<%(locus_g)s_clones>\d+)\s+(?P<%(locus_g)s_av_reads>[0-9.]+)\s*.n'
% {
'locus': locus_regex,
'locus_g': locus_group
}
]
json_paths = {
'result_file': {
'main_clone': '/clones[0]/name',
'main_clone_reads': '/clones[0]/reads[0]'
},
'fused_file': {
'reads distribution [>= 10%]': 'reads/distribution/0.1',
'reads distribution [>= 1% < 10%]': 'reads/distribution/0.01',
'reads distribution [>= .01% < 1%]': 'reads/distribution/0.001',
'reads distribution [>= .001% < .01%]':
'reads/distribution/0.0001',
'reads distribution [>= .0001% < .001%]':
'reads/distribution/0.00001',
'producer': 'samples/producer'
}
}
keys_patient = ['info']
keys_file = ['sampling_date', 'size_file']
keys = []
keys += keys_file
keys += keys_patient
regex = []
for sr in stats_regex:
r = re.compile(sr)
regex += [r]
keys += r.groupindex.keys()
keys += sorted(json_paths['result_file'].keys() +
json_paths['fused_file'].keys())
for row in d['query']:
found = {}
results_f = row.results_file.data_file
row_result = vidjil_utils.search_first_regex_in_file(
regex, defs.DIR_RESULTS + results_f, STATS_READLINES)
try:
row_result_json = vidjil_utils.extract_fields_from_json(
json_paths['result_file'], None, defs.DIR_RESULTS + results_f,
STATS_MAXBYTES)
except:
row_result_json = []
fused_file = db((db.fused_file.sample_set_id == row.sample_set.id) & (
db.fused_file.config_id == row.results_file.config_id)).select(
orderby=~db.fused_file.id, limitby=(0, 1))
if len(fused_file
) > 0 and fused_file[0].sequence_file_list is not None:
sequence_file_list = fused_file[0].sequence_file_list.split('_')
try:
pos_in_list = sequence_file_list.index(
str(row.sequence_file.id))
row_fused = vidjil_utils.extract_fields_from_json(
json_paths['fused_file'], pos_in_list,
defs.DIR_RESULTS + fused_file[0].fused_file,
STATS_MAXBYTES)
except ValueError:
row_fused = []
else:
row_fused = {}
results_list = [row_result, row_result_json, row_fused]
for key in keys:
for map_result in results_list:
if key in map_result:
row[key] = map_result[key]
found[key] = True
if key not in found:
if key in keys_patient:
row[key] = row.patient[key]
found[key] = True
elif key in keys_file:
row[key] = row.sequence_file[key]
found[key] = True
else:
row[key] = ''
# Re-process some data
keys += ['IGH_av_clones']
for row in d['query']:
row['IGH_av_clones'] = ''
if 'IGH_av_reads' in row:
try:
row['IGH_av_clones'] = '%.4f' % (1.0 /
float(row['IGH_av_reads']))
found['IGH_av_clones'] = True
except:
pass
# Keep only non-empty columns
d['stats'] = []
for key in keys:
if key in found:
d['stats'] += [key]
log.debug("patient/stats (%.3fs) %s" %
(time.time() - start, request.vars["filter"]))
return d
def stats():
start = time.time()
d = custom()
stats_regex = [
# found 771265 40-windows in 2620561 segments (85.4%) inside 3068713 sequences # before 1f501e13 (-> 2015.05)
'in (?P<seg>\d+) segments \((?P<seg_ratio>.*?)\) inside (?P<reads>\d+) sequences',
# found 10750 50-windows in 13139 reads (99.9% of 13153 reads)
'windows in (?P<seg>\d+) reads \((?P<seg_ratio>.*?) of (?P<reads>\d+) reads\)',
# segmentation causes
'log.* SEG_[+].*?-> (?P<SEG_plus>.*?).n',
'log.* SEG_[-].*?-> (?P<SEG_minus>.*?).n',
]
# stats by locus
for locus in defs.LOCUS:
locus_regex = locus.replace('+', '[+]')
locus_group = locus.replace('+', 'p')
stats_regex += [ 'log.* %(locus)s.*?->\s*?(?P<%(locus_g)s_reads>\d+)\s+(?P<%(locus_g)s_av_len>[0-9.]+)\s+(?P<%(locus_g)s_clones>\d+)\s+(?P<%(locus_g)s_av_reads>[0-9.]+)\s*.n'
% { 'locus': locus_regex, 'locus_g': locus_group } ]
json_paths = {
'result_file': {
'main_clone': '/clones[0]/name',
'main_clone_reads': '/clones[0]/reads[0]'
},
'fused_file': {
'reads distribution [>= 10%]': 'reads/distribution/0.1',
'reads distribution [>= 1% < 10%]': 'reads/distribution/0.01',
'reads distribution [>= .01% < 1%]': 'reads/distribution/0.001',
'reads distribution [>= .001% < .01%]': 'reads/distribution/0.0001',
'reads distribution [>= .0001% < .001%]': 'reads/distribution/0.00001',
'producer': 'samples/producer'
}
}
keys_patient = [ 'info' ]
keys_file = [ 'sampling_date', 'size_file' ]
keys = []
keys += keys_file
keys += keys_patient
regex = []
for sr in stats_regex:
r = re.compile(sr)
regex += [r]
keys += r.groupindex.keys()
keys += sorted(json_paths['result_file'].keys() + json_paths['fused_file'].keys())
for row in d['query']:
found = {}
results_f = row.results_file.data_file
row_result = vidjil_utils.search_first_regex_in_file(regex, defs.DIR_RESULTS + results_f, STATS_READLINES)
try:
row_result_json = vidjil_utils.extract_fields_from_json(json_paths['result_file'], None, defs.DIR_RESULTS + results_f, STATS_MAXBYTES)
except:
row_result_json = []
fused_file = db((db.fused_file.sample_set_id == row.sample_set.id) & (db.fused_file.config_id == row.results_file.config_id)).select(orderby = ~db.fused_file.id, limitby=(0,1))
if len(fused_file) > 0 and fused_file[0].sequence_file_list is not None:
sequence_file_list = fused_file[0].sequence_file_list.split('_')
try:
pos_in_list = sequence_file_list.index(str(row.sequence_file.id))
row_fused = vidjil_utils.extract_fields_from_json(json_paths['fused_file'], pos_in_list, defs.DIR_RESULTS + fused_file[0].fused_file, STATS_MAXBYTES)
except ValueError:
row_fused = []
else:
row_fused = {}
results_list = [row_result, row_result_json, row_fused]
for key in keys:
for map_result in results_list:
if key in map_result:
row[key] = map_result[key]
found[key] = True
if key not in found:
if key in keys_patient:
row[key] = row.patient[key]
found[key] = True
elif key in keys_file:
row[key] = row.sequence_file[key]
found[key] = True
else:
row[key] = ''
# Re-process some data
keys += ['IGH_av_clones']
for row in d['query']:
row['IGH_av_clones'] = ''
if 'IGH_av_reads' in row:
try:
row['IGH_av_clones'] = '%.4f' % (1.0 / float(row['IGH_av_reads']))
found['IGH_av_clones'] = True
except:
pass
# Keep only non-empty columns
d['stats'] = []
for key in keys:
if key in found:
d['stats'] += [key]
log.debug("patient/stats (%.3fs) %s" % (time.time()-start, request.vars["filter"]))
return d
