Release 0.2.4

* Bugfix: ribocount now returns correct read counts if an offset is
* provided.
* Bugfix: Don't include read counts in the longest ORF start or stop
* positions
  i.e., only include reads upstream or downstream of the start or stop
positions.

HISTORY.rst

@@ -2,6 +2,12 @@
 
 History
 =======
+0.2.4 (2015-11-25)
+------------------
+* Bugfix: ribocount now returns correct read counts if an offset is provided.
+* Bugfix: Don't include read counts in the longest ORF start or stop positions
+  i.e., only include reads upstream or downstream of the start or stop positions.
+
 0.2.3 (2015-11-24)
 ------------------
 * Bugfix: Recalculate read frame positions after applying offset.

riboplot/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = 'Vimalkumar Velayudhan'
 __email__ = '[email protected]'
-__version__ = '0.2.3'
+__version__ = '0.2.4'

riboplot/ribocore.py

@@ -244,12 +244,12 @@ def filter_ribo_counts(counts, orf_start=None, orf_stop=None):
                 filtered_counts.pop(position)
         elif orf_start:
             # check if current position is upstream of ORF start. if not, remove
-            if position > orf_start:
+            if position >= orf_start:
                 filtered_counts.pop(position)
         elif orf_stop:
             # check if current position is downstream of ORF stop. If not,
             # remove
-            if position < orf_stop:
+            if position <= orf_stop:
                 filtered_counts.pop(position)
 
     # calculate total reads for this transcript

riboplot/ribocount.py

@@ -97,10 +97,12 @@ def main(args):
 
         log.info('Get RiboSeq read counts for all transcripts in FASTA')
         for transcript in f.references:
-            ribo_counts, ribo_reads = ribocore.get_ribo_counts(b, transcript, read_length)
+            ribo_counts, ribo_reads = ribocore.get_ribo_counts(ribo_fileobj=b, transcript_name=transcript,
+                                                               read_length=read_length, read_offset=read_offset)
             if not ribo_reads:  # no reads for this transcript. skip.
                 continue
 
+            transcript_sequence = f[transcript]
             # By default, all counts will be written (ribo_counts)
             # If 5' or 3' counts requested, filter and use
             # those counts for printing instead
@@ -113,7 +115,7 @@ def main(args):
             if count_five or count_three:
                 # use default start and stop codons and find ORFs in all 3
                 # frames (+)
-                orfs = ribocore.get_three_frame_orfs(sequence=f[transcript])
+                orfs = ribocore.get_three_frame_orfs(sequence=transcript_sequence)
                 if not len(orfs):
                     log.debug('No ORFs for transcript {0}'.format(transcript))
                     continue
@@ -136,13 +138,14 @@ def main(args):
             count += 1
             csv_file = 'RiboCounts{}.csv'.format(count)
             with open(os.path.join(csv_dir, csv_file), 'w') as cw:
-                cw.write('"Position","Frame 1","Frame 2","Frame 3"\n')
-                for pos in range(1, len(f[transcript]) + 1):
+                cw.write('"Position","Nucleotide","Frame 1","Frame 2","Frame 3"\n')
+                for pos in range(1, len(transcript_sequence) + 1):
+                    nucleotide = transcript_sequence[pos - 1]
                     if pos in write_counts:
-                        cw.write('{0},{1},{2},{3}\n'.format(
-                            pos, write_counts[pos][1], write_counts[pos][2], write_counts[pos][3]))
+                        cw.write('{0},{1},{2},{3},{4}\n'.format(
+                            pos, nucleotide, write_counts[pos][1], write_counts[pos][2], write_counts[pos][3]))
                     else:
-                        cw.write('{0},{1},{2},{3}\n'.format(pos, 0, 0, 0))
+                        cw.write('{0},{1},{2},{3},{4}\n'.format(pos, nucleotide, 0, 0, 0))
             # HTML table
             table_body += '<tr><td>{0}</td><td>{1}</td>'.format(transcript, ribo_reads)
             if count_five:

riboplot/riboplot.py

@@ -174,7 +174,6 @@ def plot_profile(ribo_counts, transcript_name, transcript_length,
                    edgecolor=colors['rna'], label='RNA')
         ax_rna.set_zorder(1)
 
-#    import pudb;pudb.set_trace();
     frame_counts = {1: {}, 2: {}, 3: {}}
     for k, v in ribo_counts.iteritems():
         for fr in (1, 2, 3):
@@ -191,9 +190,6 @@ def plot_profile(ribo_counts, transcript_name, transcript_length,
 
     for frame in (1, 2, 3):
         color = colors['frames'][frame - 1]
-#        if read_offset:
-#            x_vals = [pos + read_offset for pos in frame_counts[frame].keys()]
-#        else:
         x_vals = frame_counts[frame].keys()
         ax2.bar(x_vals, frame_counts[frame].values(), color=color, facecolor=color, edgecolor=color)
 
@@ -383,7 +379,7 @@ def main(args):
 
         log.info('Writing RiboSeq read counts for {}'.format(transcript_name))
         with open(os.path.join(output_path, 'RiboCounts.csv'), 'w') as f:
-            f.write('"Position","Sequence","Frame 1","Frame 2","Frame 3"\n')
+            f.write('"Position","Nucleotide","Frame 1","Frame 2","Frame 3"\n')
 
             for pos in range(1, transcript_length + 1):
                 if pos in ribo_counts:

setup.py

@@ -22,7 +22,7 @@
 
 setup(
     name='riboplot',
-    version='0.2.3',
+    version='0.2.4',
     description="Plot read counts of RiboSeq data from BAM format alignment files",
     long_description=readme + '\n\n' + history,
     author="Vimalkumar Velayudhan",