From e35a0b01cfc692025422b04eabf08fbf59e9afa4 Mon Sep 17 00:00:00 2001 From: Andrey Prjibelski Date: Fri, 2 Aug 2024 01:52:27 +0300 Subject: [PATCH] nested with --- src/long_read_counter.py | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/src/long_read_counter.py b/src/long_read_counter.py index 7e489090..a5f5177a 100644 --- a/src/long_read_counter.py +++ b/src/long_read_counter.py @@ -363,23 +363,23 @@ def dump_ungrouped(self, all_features): f.write("__usable\t%d\n" % self.reads_for_tpm) def dump_grouped(self, all_features, all_groups): - with (self.get_output_file_handler() as output_file, - self.get_linear_output_file_handler() as linear_output_file): - assert linear_output_file is not None - - output_file.write(self.format_header(all_groups)) - linear_output_file.write("#feature_id\tgroup_id\tcount\n") - for feature_id in all_features: - row_count = 0 - for group_id in self.feature_counter[feature_id].data.keys(): - count = self.feature_counter[feature_id].data[group_id] - linear_output_file.write("%s\t%s\t%.2f\n" % (feature_id, self.ordered_groups[group_id], count)) - row_count += count - if not self.output_zeroes and row_count == 0: - continue - count_values = [self.feature_counter[feature_id].get(self.group_numeric_ids[group_id]) for group_id in - all_groups] - output_file.write("%s\t%s\n" % (feature_id, "\t".join(["%.2f" % c for c in count_values]))) + with self.get_output_file_handler() as output_file: + with self.get_linear_output_file_handler() as linear_output_file: + assert linear_output_file is not None + + output_file.write(self.format_header(all_groups)) + linear_output_file.write("#feature_id\tgroup_id\tcount\n") + for feature_id in all_features: + row_count = 0 + for group_id in self.feature_counter[feature_id].data.keys(): + count = self.feature_counter[feature_id].data[group_id] + linear_output_file.write("%s\t%s\t%.2f\n" % (feature_id, self.ordered_groups[group_id], count)) + row_count += count + if not self.output_zeroes and row_count == 0: + continue + count_values = [self.feature_counter[feature_id].get(self.group_numeric_ids[group_id]) for group_id in + all_groups] + output_file.write("%s\t%s\n" % (feature_id, "\t".join(["%.2f" % c for c in count_values]))) def convert_counts_to_tpm(self, normalization_str=NormalizationMethod.simple.name): normalization = NormalizationMethod[normalization_str]