[med-svn] [mapping-pipeline] 07/10: Use 2to3 to make sure script will properly run with Python3

[Andreas Tille]

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tille pushed a commit to branch master
in repository mapping-pipeline.

commit 8ed4e2d4a41277abc20f292d1ddbbb965bb3c88f
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 21 12:38:16 2017 +0100

    Use 2to3 to make sure script will properly run with Python3
---
 debian/patches/python3.patch | 61 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 59 insertions(+), 2 deletions(-)

diff --git a/debian/patches/python3.patch b/debian/patches/python3.patch
index a5ad17b..91b1993 100644
--- a/debian/patches/python3.patch
+++ b/debian/patches/python3.patch
@@ -2,12 +2,69 @@ Author: Andreas Tille
 Last-Update: Mon, 12 Dec 2016 13:19:31 +0100
 Description: This script should not be called directly
  (and if ever not with Python but rather Python3)
+ .
+ The diff was created using 2to3.
 
 --- a/metrics.py
 +++ b/metrics.py
-@@ -1,5 +1,3 @@
+@@ -1,6 +1,4 @@
 -#!/usr/bin/env python
 -
- import custom_logger as log
+-import custom_logger as log
++from . import custom_logger as log
  import numpy as np
  import matplotlib
+ matplotlib.use('Agg')
+@@ -120,7 +118,7 @@ class METRICS:
+                 self.reads_per_quality_result.append([os.path.realpath(os.path.join(self.output, 'reads_per_quality_{}.pdf'.format(valid_filename(reference)))), reference.replace('_','\_')])
+                 fig, ax = plt.subplots( nrows=1, ncols=1 )  # create figure & 1 axis
+                 ax.set_yscale('symlog')
+-                ax.bar(range(rpq.size), rpq, align='center')
++                ax.bar(list(range(rpq.size)), rpq, align='center')
+                 pylab.xlim([-0.5,rpq.size-0.5])
+                 pylab.ylim(ymin=-0.05)
+                 ax.set_xlabel('Mapping quality')
+@@ -204,7 +202,7 @@ class METRICS:
+             # Count how often a coverage appears. bincount[coverage]=#coverage
+             bases_per_coverage = np.bincount(reference_coverage)
+             # Bin the coverages into 1000 bin and calculate the mean for every bin.
+-            binned_coverage = stats.binned_statistic(range(bases_per_coverage.size), bases_per_coverage, statistic = self._integer_mean, bins = 1000)[0]
++            binned_coverage = stats.binned_statistic(list(range(bases_per_coverage.size)), bases_per_coverage, statistic = self._integer_mean, bins = 1000)[0]
+             # Trim again in case the maximal coverage is less than 1000.
+             binned_coverage = np.trim_zeros(binned_coverage, 'b')
+             # Get the number of binned coverages.
+@@ -219,7 +217,7 @@ class METRICS:
+                         factor = float(bases_per_coverage.size)/len_coverage
+                         self._set_axis(ax, factor)
+                     ax.set_yscale('symlog')
+-                    ax.bar(range(len_coverage), binned_coverage, align='center', color='b', linewidth=0, edgecolor='b')
++                    ax.bar(list(range(len_coverage)), binned_coverage, align='center', color='b', linewidth=0, edgecolor='b')
+                     pylab.xlim([-0.005*len_coverage, len_coverage+0.005*len_coverage])
+                     ax.set_xlabel('Coverage')
+                     ax.set_ylabel('Base Count')
+@@ -263,9 +261,9 @@ class METRICS:
+                         factor = float(reference_coverage.size)/len_reference
+                         self._set_axis(ax, factor)
+                     ax.set_yscale('symlog')
+-                    ax.plot(range(len_reference), reference_coverage_mean, 'r', label='mean')
+-                    ax.plot(range(len_reference), reference_coverage_max, 'b', label='max')
+-                    ax.plot(range(len_reference), reference_coverage_min, 'g', label='min')
++                    ax.plot(list(range(len_reference)), reference_coverage_mean, 'r', label='mean')
++                    ax.plot(list(range(len_reference)), reference_coverage_max, 'b', label='max')
++                    ax.plot(list(range(len_reference)), reference_coverage_min, 'g', label='min')
+                     ax.legend(bbox_to_anchor=(0., 1.05, 1., .102), loc=3, ncol=3, mode="expand", borderaxespad=0.)
+                     ax.set_xlabel('Position')
+                     ax.set_ylabel('Coverage')
+@@ -310,9 +308,9 @@ class METRICS:
+                         factor = float(reference_mapq.size)/len_reference
+                         self._set_axis(ax, factor)
+                     #self.ax.set_yscale('symlog')
+-                    ax.plot(range(len_reference), reference_mapq_mean, 'r', label='mean')
+-                    ax.plot(range(len_reference), reference_mapq_max, 'b', label='max')
+-                    ax.plot(range(len_reference), reference_mapq_min, 'g', label='min')
++                    ax.plot(list(range(len_reference)), reference_mapq_mean, 'r', label='mean')
++                    ax.plot(list(range(len_reference)), reference_mapq_max, 'b', label='max')
++                    ax.plot(list(range(len_reference)), reference_mapq_min, 'g', label='min')
+                     ax.legend(bbox_to_anchor=(0., 1.05, 1., .102), loc=3, ncol=3, mode="expand", borderaxespad=0.)
+                     ax.set_xlabel('Position')
+                     ax.set_ylabel('Mapping Quality')

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