updated setup.py and README

cancerit · May 8, 2018 · a73c5cc · a73c5cc
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Showing 5 changed files with 9 additions and 6 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,6 +1,8 @@
 # CHANGES
 ## 1.1.1
  * Added segmentation module in setup.py
+ * added requirements.txt file
+ * Corrected broken links in README
 
 ## 1.1.0
  * Additional output formats for normalised and corrected counts

diff --git a/pyCRISPRcleanR.egg-info/requires.txt b/pyCRISPRcleanR.egg-info/requires.txt
@@ -2,3 +2,4 @@ rpy2
 pandas
 numpy
 plotly
+tzlocal
diff --git a/pyCRISPRcleanR/staticMethods.py b/pyCRISPRcleanR/staticMethods.py
@@ -150,8 +150,8 @@ def process_segments(cbs_dict, ignored_genes, min_genes, controls, no_rep, outdi
             cnarr['correction'] = 0
             cnarr['correctedFC'] = cnarr.avgFC
             n_genes_in_seg = 0
-            reverted_counts = cnarr.iloc[:, cnarr.columns.get_loc('end') +
-                                        controls + 1:cnarr.columns.get_loc('avgFC')]
+            reverted_counts = cnarr.iloc[:, cnarr.columns.get_loc('end') + controls + 1:
+                                        cnarr.columns.get_loc('avgFC')]
 
             for segment in segrows.itertuples():
                 idxs = list(range(segment.startRow - 1, segment.endRow))
@@ -202,8 +202,8 @@ def _correct_counts(segdata, controls, no_rep):
         c = nc.mean(axis=1)
         n = segdata.correctedFC
         reverted['revc'] = c * (pow(2, n))
-        normed_num = segdata.iloc[:, segdata.columns.get_loc('end') +
-                                controls + 1:segdata.columns.get_loc('avgFC')]
+        normed_num = segdata.iloc[:, segdata.columns.get_loc('end') + controls + 1:
+                                segdata.columns.get_loc('avgFC')]
         normed_num += 1
         proportions = normed_num.div(normed_num.agg('sum', axis=1), axis=0)
         reverted = reverted * no_rep

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-tzlocal
+tzlocal==1.5.1
 numpy==1.14.3
 pandas==0.22.0
 rpy2==2.9.3

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
     'author_email': '[email protected]',
     'python_requires': '>= 3.3',
     'setup_requires': ['pytest','pytest-cover'],
-    'install_requires': ['rpy2', 'pandas', 'numpy', 'plotly'],
+    'install_requires': ['rpy2', 'pandas', 'numpy', 'plotly', 'tzlocal'],
     'packages': ['pyCRISPRcleanR'],
     'package_data': {'pyCRISPRcleanR':['config/*.conf','segmentation/*.py']},
     'entry_points': {
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,3 +2,4 @@ rpy2 @@
     pandas
     numpy
     plotly
+    tzlocal