def main(countsfile, outpath, countsfile2, strand_symmetry, force_overwrite,
dry_run, verbose):
args = locals()
table = LoadTable(countsfile, sep='\t')
if not dry_run:
log_file_path = os.path.join(util.abspath(outpath),
'spectra_analysis.log')
LOGGER.log_file_path = log_file_path
LOGGER.log_message(str(args), label='vars')
LOGGER.input_file(countsfile)
# if there's a strand symmetry argument then we don't need a second file
if strand_symmetry:
group_label = 'strand'
counts_table = util.spectra_table(table, group_label)
if not strand_symmetry:
group_label = 'group'
# be sure there's two files
counts_table2 = LoadTable(countsfile2, sep='\t')
LOGGER.input_file(countsfile2)
counts_table2 = counts_table2.with_new_column('group',
lambda x: '2', columns=counts_table2.header[0])
counts_table1 = table.with_new_column('group',
lambda x: '1', columns=table.header[0])
counts_table1 = util.spectra_table(counts_table1, group_label)
counts_table2 = util.spectra_table(counts_table2, group_label)
# now combine
header = ['group'] + counts_table2.header[:-1]
raw1 = counts_table1.tolist(header)
raw2 = counts_table2.tolist(header)
counts_table = LoadTable(header=header, rows=raw1 + raw2)
if verbose:
print(counts_table)
# spectra table has [count, start, end, group] order
# we reduce comparisons to a start base
results = []
saveable = {}
for start_base in counts_table.distinct_values('start'):
subtable = counts_table.filtered('start == "%s"' % start_base)
columns = [c for c in counts_table.header if c != 'start']
subtable = subtable.get_columns(columns)
total_re, dev, df, collated, formula = log_lin.spectra_difference(
subtable, group_label)
r = [list(x) for x in collated.to_records(index=False)]
if not strand_symmetry:
grp_labels = {'1': countsfile,
'2': countsfile2}
grp_index = list(collated.columns).index('group')
for row in r:
row[grp_index] = grp_labels[row[grp_index]]
p = chisqprob(dev, df)
if p < 1e-6:
prob = "%.2e" % p
else:
prob = "%.6f" % p
for row in r:
row.insert(0, start_base)
row.append(prob)
results += r
significance = ["RE=%.6f" % total_re, "Dev=%.2f" % dev, "df=%d" % df,
"p=%s" % p]
stats = " : ".join(significance)
print("Start base=%s %s" % (start_base, stats))
saveable[start_base] = dict(rel_entropy=total_re, deviance=dev,
df=df, prob=p,
formula=formula, stats=collated.to_json())
table = LoadTable(header=['start_base'] + list(collated.columns) +
['prob'],
rows=results, digits=5).sorted(columns='ret')
json_path = None
outpath = util.abspath(outpath)
if not dry_run:
util.makedirs(outpath)
json_path = os.path.join(outpath, 'spectra_analysis.json')
dump_json(saveable, json_path)
LOGGER.output_file(json_path)
table_path = os.path.join(outpath, 'spectra_summary.txt')
table.write(table_path, sep='\t')
LOGGER.output_file(table_path)
LOGGER.log_message(str(significance), label="significance")
def main(counts_pattern, output_path, strand_symmetric, split_dir, dry_run,
force_overwrite):
"""export tab delimited combined counts table by appending the 12 mutation
direction tables, adding a new column ``direction``."""
args = locals()
output_path = abspath(output_path)
if strand_symmetric and split_dir:
split_dir = abspath(split_dir)
else:
split_dir = None
# check we the glob pattern produces the correct number of files
counts_files = glob.glob(counts_pattern)
check_found_filenames(counts_files)
counts_filename = os.path.join(output_path, 'combined_counts.txt')
runlog_path = os.path.join(output_path, "combined_counts.log")
if not dry_run:
if not force_overwrite and (os.path.exists(counts_filename)
or os.path.exists(runlog_path)):
msg = "Either %s or %s already exist. Force overwrite of "\
"existing files with -F."
raise ValueError(msg % (counts_filename, runlog_path))
makedirs(output_path)
if split_dir:
makedirs(split_dir)
LOGGER.log_file_path = runlog_path
LOGGER.log_message(str(args), label='vars')
for fn in counts_files:
LOGGER.input_file(fn, label="count_file")
start_time = time.time()
# run the program
all_counts = []
header = None
num_rows = 0
basenames = []
for fn in counts_files:
basenames.append(os.path.basename(fn))
mutation = direction.findall(fn)[0]
table = LoadTable(fn, sep='\t')
if header is None:
header = list(table.header)
header.append('direction')
num_rows = table.shape[0]
data = table.tolist()
new = []
for row in data:
row.append(mutation)
new.append(row)
all_counts += new
table = LoadTable(header=header, rows=all_counts)
if strand_symmetric:
table = make_strand_symmetric_table(table)
if split_dir:
group_subtables = get_subtables(table, group_label='direction')
if not dry_run:
table.write(counts_filename, sep='\t')
LOGGER.output_file(counts_filename)
if split_dir:
for group, subtable in group_subtables:
# we first assume that group is part of the filenames!
fn = [bn for bn in basenames if group in bn]
if len(fn) == 1:
fn = fn[0]
else:
fn = "%s.txt" % group
counts_filename = os.path.join(split_dir, fn)
subtable.write(counts_filename, sep='\t')
LOGGER.output_file(counts_filename)
# determine runtime
duration = time.time() - start_time
if not dry_run:
LOGGER.log_message("%.2f" % (duration / 60.),
label="run duration (minutes)")
print("Done!")