From f8e9bc129355406e5bba22835f92ee813d94c6f1 Mon Sep 17 00:00:00 2001 From: "y.hoogstrate@erasmusmc.nl" Date: Tue, 5 Apr 2016 15:30:43 +0200 Subject: [PATCH 1/2] Better progression logging - never skips 100% --- fuma/ComparisonTriangle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fuma/ComparisonTriangle.py b/fuma/ComparisonTriangle.py index 636870b..4827dc2 100644 --- a/fuma/ComparisonTriangle.py +++ b/fuma/ComparisonTriangle.py @@ -148,7 +148,7 @@ def prune_duplicates(self,merged_fusions): def log_progress(self,n_total, passed, previous_percentage): # Print percentage - doesn't entirely fit yet percentage = 100.0 * (float(passed) / float(n_total)) - if percentage >= previous_percentage + 5.0:# Repport each 5% + if percentage >= previous_percentage + 5.0 or passed == n_total:# Repport each 5% self.logger.debug(str(round(percentage,1))+"% completed") previous_percentage = percentage return n_total, passed, previous_percentage From 99f4fbfc9b7ffbd232ec79811f24f540f3949229 Mon Sep 17 00:00:00 2001 From: "y.hoogstrate@erasmusmc.nl" Date: Tue, 5 Apr 2016 16:26:23 +0200 Subject: [PATCH 2/2] Output in the order of number of datasets in which fusion gene is found --- Changelog | 9 +++++++++ fuma/ComparisonTriangle.py | 6 +++--- fuma/__init__.py | 2 +- 3 files changed, 13 insertions(+), 4 deletions(-) diff --git a/Changelog b/Changelog index 6bf2cd7..c3923a3 100644 --- a/Changelog +++ b/Changelog @@ -1,3 +1,12 @@ +2016-04-05 Youri Hoogstrate + + * Version 3.0.1: Added a simple break statement ensures that the output is + in the order of the number of datasets in which a fusion gene is being + found. + + The logging function now does not skip the 100.0% which was caused in some + cases occured due to a rounding artefact. + 2016-04-01 Youri Hoogstrate * Version 3.0.0: The core has been rewritte because it needed to use much diff --git a/fuma/ComparisonTriangle.py b/fuma/ComparisonTriangle.py index 4827dc2..b7586bf 100644 --- a/fuma/ComparisonTriangle.py +++ b/fuma/ComparisonTriangle.py @@ -110,8 +110,8 @@ def overlay_fusions_recursive(self,fh,merged_fusions): export_fusions = [tmp for tmp in merged_fusions] merged_fusions_new = [] - for y,fusion_y in self: - for x in range(len(merged_fusions)): + for x in range(len(merged_fusions)): + for y,fusion_y in self: merged_fusion_x = merged_fusions[x] n_total, passed, previous_percentage = self.log_progress(n_total, passed, previous_percentage) @@ -122,9 +122,9 @@ def overlay_fusions_recursive(self,fh,merged_fusions): if comparison != False: export_fusions[x] = None merged_fusions_new.append(comparison) + break passed += 1 - n_total, passed, previous_percentage = self.log_progress(n_total, passed, previous_percentage) merged_fusions_new = self.prune_duplicates(merged_fusions_new) diff --git a/fuma/__init__.py b/fuma/__init__.py index 68bb952..13211a6 100644 --- a/fuma/__init__.py +++ b/fuma/__init__.py @@ -21,7 +21,7 @@ """ -__version_info__ = ('3', '0', '0') +__version_info__ = ('3', '0', '1') __version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3])+"-"+__version_info__[3] __author__ = 'Youri Hoogstrate' __homepage__ = 'https://github.com/yhoogstrate/fuma'