From 861a955dae4a73b8ade99d48015d677959d39a0b Mon Sep 17 00:00:00 2001
From: zhpn1024 <zhpn1024@163.com>
Date: Wed, 18 Nov 2020 21:43:49 +0800
Subject: [PATCH] v0.2.6

---
 CHANGELOG       | 10 ++++++++++
 README.rst      | 15 +++++++++++++--
 bin/ribotish    |  2 +-
 setup.py        |  2 +-
 src/__init__.py |  2 +-
 src/zbio/fa.py  |  3 ++-
 6 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index 5f174f8..04b8e53 100755
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,13 @@
+2020-11-15 ribotish 0.2.6
+
+	Add --inframecount option in predict to report in-frame RPF counts.
+
+	Add --end3 option in quality to plot 3' end profiles.
+
+	Fix gff problems.
+
+	Fix problem of genome position at the start/stop of downstream/upstream exon.
+
 2020-4-19 ribotish 0.2.5
 
 	Fix negative start error.
diff --git a/README.rst b/README.rst
index c7beef8..7093e88 100755
--- a/README.rst
+++ b/README.rst
@@ -1,6 +1,6 @@
-README for Ribo-TISH (0.2.5)
+README for Ribo-TISH (0.2.6)
 ==================================
-<2019-12-9 Peng Zhang>
+<2020-11-15 Peng Zhang>
 
 Introduction
 ============
@@ -139,6 +139,11 @@ Not consider reads with mismatch at position 0 (5' end mismatch) as a new group.
 
 Threshold for quality. Default: 0.5. Group that frame bias ratio < TH will be considered as low quality and this group of reads will not be used in further analysis. The offset for low quality groups will not be set in parameter file.
 
+--end3
+``````````
+
+Plot RPF 3' end profile instead of 5' end.
+
 --colorblind
 ````````````
 
@@ -441,6 +446,12 @@ Report amino acid sequences.
 
 Report all exon block positions for predicted ORFs. Format: start1-stop1,start2-stop2,...startN-stopN. In chromosome direction.
 
+--inframecount
+``````````````
+
+Report the sum of all counts at the in-frame positions in the ORF.
+
+
 Output files
 ------------
 
diff --git a/bin/ribotish b/bin/ribotish
index ec14236..33c0b11 100755
--- a/bin/ribotish
+++ b/bin/ribotish
@@ -6,7 +6,7 @@ This code is free software; you can redistribute it and/or modify it
 under the terms of the BSD License (see the file COPYING included with
 the distribution).
 @status: Beta
-@version: 0.2.5
+@version: 0.2.6
 @author:  Peng Zhang
 @contact: zhpn1024@163.com
 """
diff --git a/setup.py b/setup.py
index c9177d0..d066614 100755
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
 # the distribution).
 # 
 # @status:  Beta
-# @version: 0.2.5
+# @version: 0.2.6
 # @author:  Peng Zhang
 # @contact: zhpn1024@163.com
 
diff --git a/src/__init__.py b/src/__init__.py
index d730c9a..3856c29 100755
--- a/src/__init__.py
+++ b/src/__init__.py
@@ -1,2 +1,2 @@
 __all__=["run"]
-__version__ = '0.2.5'
+__version__ = '0.2.6'
diff --git a/src/zbio/fa.py b/src/zbio/fa.py
index 20e5d03..e4bdf4d 100755
--- a/src/zbio/fa.py
+++ b/src/zbio/fa.py
@@ -23,6 +23,7 @@ def faIter(file, protein = False):
 def rc(seq):
   '''reverse complement
   '''
+  if seq is None: return None
   comps = {'A':"T", 'C':"G", 'G':"C", 'T':"A",
        'B':"V", 'D':"H", 'H':"D", 'K':"M",
        'M':"K", 'R':"Y", 'V':"B", 'Y':"R",
@@ -32,7 +33,7 @@ def rc(seq):
 def changechr(chr):
   '''change between two chr versions
   '''
-  if chr.isdigit() or chr in ('X','Y','M'): return 'chr' + chr
+  if chr[0].isdigit() or chr in ('X','Y','M'): return 'chr' + chr
   elif chr == 'MT' : return 'chrM'
   elif chr == 'chrM' : return 'MT'
   elif chr[0:3] == 'chr' : return chr[3:]