v0.2.6

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.

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
 ------------
 

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
 """

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
 

src/__init__.py

@@ -1,2 +1,2 @@
 __all__=["run"]
-__version__ = '0.2.5'
+__version__ = '0.2.6'

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:]