def PredictionAnalysis(align1, align2, outfile, granular = True, open_mode = 'w', limit_functions = set(), **kwargs):
a1 = Alignment.alignment_from_file(align1)
a2 = Alignment.alignment_from_file(align2)
print 'loaded alignments'
sprot = prot_from_path(align1)
tprot = prot_from_path(align2)
defaults = dict(zip(LinkFields.LINK_FIELDS, [None]*len(LinkFields.LINK_FIELDS)))
defaults['S1-Prot']=sprot
defaults['S2-Prot']=tprot
defaults.pop('Source-Start')
defaults.pop('Source-End')
defaults.pop('Target-Start')
defaults.pop('Target-End')
calculator = LinkUtils.LinkCalculator()
rmheaders = dict((head, None) for head in calculator.get_fields())
submats = LinkUtils.get_all_sub_mats()
ohandle = open(outfile, open_mode)
owriter = csv.DictWriter(ohandle, LinkFields.LINK_FIELDS,
delimiter = '\t', extrasaction='ignore')
if open_mode == 'w':
owriter.writerow(dict(zip(LinkFields.LINK_FIELDS,
LinkFields.LINK_FIELDS)))
done = set()
else:
done = get_done(outfile)
if granular:
for row in task_loader(None, a1, a2, defaults,submats, 50, align1==align2, limit_functions=limit_functions, found_items = done):
owriter.writerows(convert_row_to_writeable_rows(row, rmheaders))
else:
process_que = Queue(1000)
loader = Thread(target=task_loader,
args= (process_que, a1, a2, defaults,submats, 50, align1==align2),
kwargs={'limit_functions':limit_functions, 'found_items': done})
loader.start()
print 'waiting for first'
item = process_que.get()
while item is not None:
try:
row = item.get(timeout = 60*30, interval = 60*1)
except TimeoutError:
logging.warning('no result for one!')
item = process_que.get()
continue
logging.info('%i %i' % (row['S1-Start'], row['S2-End']))
owriter.writerows(convert_row_to_writeable_rows(row, rmheaders))
item = process_que.get()
def link_calculator(row, submats, seq1, seq2, granular = False,limit_functions = set()):
c1 = AlignUtils.make_counts(seq1)
c2 = AlignUtils.make_counts(seq2)
row['S1-Entropy'] = AlignUtils.calculate_entropy(seq1)
row['S2-Entropy'] = AlignUtils.calculate_entropy(seq2)
row['S12-Mapping'] = LinkUtils.prediction_mapping(seq1, seq2)
row['S21-Mapping'] = LinkUtils.prediction_mapping(seq2, seq1)
row['SeqLength'] = len(seq1)
row['S1-Cons'] = max(x/len(seq1) for x in c1.values())
row['S2-Cons'] = max(x/len(seq2) for x in c2.values())
if row['S1-Cons'] > 0.99999 or row['S2-Cons'] > 0.99999:
return row
logging.info('%s\t%f\t%s\t%f' % (seq1, row['S1-Cons'], seq2, row['S2-Cons']))
processfuns = []
for name, mat in submats:
if granular:
processfuns.append(('SBASC_'+name,
LinkUtils.calculate_SBASC, (mat,)))
else:
processfuns.append(('SBASC_'+name,
partial(LinkUtils.calculate_SBASC, mat), ()))
processfuns.append(('Mutual_Info', LinkUtils.calculate_mutual_info, {}))
processfuns.append(('OMES', LinkUtils.calculate_OMES, ()))
processfuns.append(('Linkage', LinkUtils.calculate_mapping, ()))
suffs = ['_raw', '_pval', '_null', '_count']
if limit_functions:
processfuns = [x for x in processfuns if x[0] in limit_functions]
for name, func, evals in processfuns:
if granular:
logging.info('calculating %s %i %i' % (name, row['S1-Start'], row['S2-Start']))
res = LinkUtils.celery_calculate_vals(seq1, seq2, func, preargs=evals)
else:
res = LinkUtils.calculate_vals(seq1, seq2, func)
for val, suff in zip(res, suffs):
row[name+suff] = val
logging.info(name+suff+':'+str(val))
return row