def report_logs(self,
name,
logs,
filter=(lambda sample, field: True),
renaming={}):
table = mine_logs(logs, filter)
if name:
filename = self.workspace / (self.file_prefix + name + '.csv')
io.write_csv_2(filename, table)
self.p(self.href(filename))
if table:
table = mine_logs(logs, filter, commas=True)
self.write('<table style="font-size: 75%">\n')
self.write('<tr>\n')
self.write('<th>Sample</th>\n')
for key in table.values()[0].keys():
self.write('<th>' + key + '</th>')
self.write('</tr>\n')
for sample, row in table.items():
self.write('<tr>\n')
self.write('<td>' + renaming.get(sample, sample) + '</td>\n')
for value in row.values():
self.write('<td>' + value + '</td>')
self.write('</tr>\n')
self.write('</table>\n')
def report_logs(self, name, logs, filter=(lambda sample, field: True), renaming={}):
table = mine_logs(logs, filter)
if name:
filename = self.workspace / (self.file_prefix + name + '.csv')
io.write_csv_2(filename, table)
self.p(self.href(filename))
if table:
table = mine_logs(logs, filter, commas=True)
self.write('<table style="font-size: 75%">\n')
self.write('<tr>\n')
self.write('<th>Sample</th>\n')
for key in table.values()[0].keys():
self.write('<th>'+key+'</th>')
self.write('</tr>\n')
for sample, row in table.items():
self.write('<tr>\n')
self.write('<td>'+renaming.get(sample,sample)+'</td>\n')
for value in row.values():
self.write('<td>'+value+'</td>')
self.write('</tr>\n')
self.write('</table>\n')
def _extract_raw(self):
work = io.Workspace(self.output_dir, must_exist=False)
raw = io.Workspace(work/'raw', must_exist=False)
for name, counts, norms in [
('genewise',
work/('expression','genewise','counts.csv'),
work/('expression','genewise','norm.csv'),
),
('primarypeakwise',
work/('expression','primarypeakwise','counts.csv'),
work/('expression','primarypeakwise','norm.csv'),
),
('peakwise',
work/('expression','peakwise','counts.csv'),
work/('expression','peakwise','norm.csv'),
),
('pairwise',
work/('peak-shift','individual-pairs.csv'),
work/('peak-shift','individual-pairs-norm.csv'),
),
]:
nesoni.Vst(
raw/(name+'-mlog2-RPM'),
counts,
norm_file = norms
).make()
counts_table = io.read_grouped_table(counts)
io.write_csv_2(raw/(name+'-info.csv'), counts_table['Annotation'])
io.write_csv_2(raw/(name+'-count.csv'), counts_table['Count'])
io.write_csv_2(raw/(name+'-tail.csv'), counts_table['Tail'])
io.write_csv_2(raw/(name+'-tail-count.csv'), counts_table['Tail_count'])
io.write_csv_2(raw/(name+'-proportion.csv'), counts_table['Proportion'])
norm_table = io.read_grouped_table(norms)
io.write_csv_2(raw/(name+'-norm.csv'), norm_table['All'])
def _extract_raw(self):
work = io.Workspace(self.output_dir, must_exist=False)
raw = io.Workspace(work/'raw', must_exist=False)
for name, counts, norms in [
('genewise',
work/('expression','genewise','counts.csv'),
work/('expression','genewise','norm.csv'),
),
('primarypeakwise',
work/('expression','primarypeakwise','counts.csv'),
work/('expression','primarypeakwise','norm.csv'),
),
('peakwise',
work/('expression','peakwise','counts.csv'),
work/('expression','peakwise','norm.csv'),
),
('pairwise',
work/('peak-shift','individual-pairs.csv'),
work/('peak-shift','individual-pairs-norm.csv'),
),
]:
nesoni.Vst(
raw/(name+'-mlog2-RPM'),
counts,
norm_file = norms
).make()
counts_table = io.read_grouped_table(counts)
io.write_csv_2(raw/(name+'-info.csv'), counts_table['Annotation'])
io.write_csv_2(raw/(name+'-count.csv'), counts_table['Count'])
io.write_csv_2(raw/(name+'-tail.csv'), counts_table['Tail'])
io.write_csv_2(raw/(name+'-tail-count.csv'), counts_table['Tail_count'])
io.write_csv_2(raw/(name+'-proportion.csv'), counts_table['Proportion'])
norm_table = io.read_grouped_table(norms)
io.write_csv_2(raw/(name+'-norm.csv'), norm_table['All'])