Differences between revisions 6 and 11 (spanning 5 versions)

Sage Interactions - Bioinformatics

Contents

Web app: protein browser FIXME

by Marshall Hampton (tested by William Stein) [sagecell-issues]

by Marshall Hampton [sagecell-issues]

-  ⇤ ← Revision 6 as of 2012-04-18 17:39:08 → 
  Size: 2873
  Editor: bvarberg
  Comment:
+   ← Revision 11 as of 2020-02-08 13:26:23 → ⇥
  Size: 2898
  Editor: chapoton
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-== Web app: protein browser ==
+== Web app: protein browser FIXME ==
 Line 8:
-sagecell-issues
+[sagecell-issues]
 Line 10:
-import urllib2 as U
+from six.moves.urllib.request import urlopen
 Line 17:
-    f = U.urlopen(gen_str + GenBank_ID)             g = f.read()
    f.close()
+    with urlopen(gen_str + GenBank_ID) as f:
        g = f.read()
-Line 26:
+Line 25:
+[sagecell-issues]
 Line 27:
-sagecell-issues
-Line 59:
+Line 58:
-    print 'Population size: ' + str(pop_size)
    print 'Selection coefficient for first taxon: ' + str(d_field(selection))
+    print('Population size: ' + str(pop_size))
    print('Selection coefficient for first taxon: ' + str(d_field(selection)))
-Line 70:
+Line 69:
-    print 'Generations until coalescence: ' + str(len(gens))
    show(coal_plot(coal_data1), axes = False, figsize = [8,4.0*len(gens)/pop_size], ymax = len(gens)-1)
+    print('Generations until coalescence: ' + str(len(gens)))
    show(coal_plot(coal_data1), axes = False, figsize = [8, 4.0*len(gens)/pop_size], ymax = len(gens)-1)