From 8a62033d73a5a08b5a588b52f25acaa51a5fe71f Mon Sep 17 00:00:00 2001 From: Annika Fust Date: Wed, 8 Nov 2017 10:37:47 +0100 Subject: [PATCH] update --- CHANGES | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGES b/CHANGES index fde16e1..3b89f23 100644 --- a/CHANGES +++ b/CHANGES @@ -1,8 +1,12 @@ +## 2.0.0-alpha (2017-11-08) + +- update uropa to python 3 format with the aid of python 2to3 + ## 1.2.1 (2017-09-07) - Rearranged package structure towards a full Pypi packages - Renamed summary.R to utils/uropa_summary.R -- Renamed reformat_output.R to utisl/uropa_reformat_output.R +- Renamed reformat_output.R to utils/uropa_reformat_output.R - Reflected changes in documentation ## 1.2.0 (2017-09-05) @@ -13,7 +17,7 @@ ## 1.1.2 (2017-09-04) -- Added proper help for auxillary R scripts (exit code 0) +- Added proper help for axillary R scripts (exit code 0) - Made call to reformat_output.R multi-threaded - Cleaned some code, added citation @@ -31,7 +35,7 @@ - Updated summary script for new gridExtra requirements (rows=NULL instead of show.rownames=FALSE) - Fixed bug in log file handling - Fixed bug in internals features, now works for distances larger than default distance -- Removed summary config after usage, removed split_peaks subdirectory in case of multithreading +- Removed summary config after usage, removed split_peaks subdirectory in case of multi threading ## 1.0 (2016-11-22) @@ -63,7 +67,7 @@ - Check for all keys not to have EMPTY values. - Check distance of p.center -gene.center,start,end for valid_dist of hit. - Fix cases of checking peak columns(make 3 'if's for diff sizes).Also read strand and replace to None if strand == ".". -- Extract attrib value one by one from all queries and give "not.found" if key doesn't exist.(get_hit_attribute) +- Extract attribute value one by one from all queries and give "not.found" if key doesn't exist.(get_hit_attribute) - When correct_dir but best_hit or All_hits already written, just "continue", no NAs bcs it overwrites best hit of same peak,or keeps NA while there is also hit. - Hits from all queries are visible in All_hits, per query, and in Best Hits the best per Query. BestBest hits table has the best of all queries. - Features of gtf are extracted and replaced as default if no key given. If wrong feat_value given ->Error proposing gtf features.