Mercurial > repos > greg > gene_family_integrator

diff utils.py @ 0:109a0eb7791f draft

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author greg
date Thu, 06 Apr 2017 13:34:02 -0400
parents
children 0dd84595cf37
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.py	Thu Apr 06 13:34:02 2017 -0400
@@ -0,0 +1,42 @@
+import os
+import shutil
+import sys
+
+
+def check_execution_errors(rc, stderr):
+    if rc != 0:
+        stop_err(stderr.read())
+
+
+def move_directory_files(source_dir, destination_dir):
+    source_directory = os.path.abspath(source_dir)
+    destination_directory = os.path.abspath(destination_dir)
+    if not os.path.isdir(destination_directory):
+        os.makedirs(destination_directory)
+    for dir_entry in os.listdir(source_directory):
+        source_entry = os.path.join(source_directory, dir_entry)
+        shutil.move(source_entry, destination_directory)
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+
+def write_html_output(output, title, dir):
+    with open(output, 'w') as fh:
+        fh.write('<html><head><h3>%s</h3></head>\n' % title)
+        fh.write('<body><p/><table cellpadding="2">\n')
+        fh.write('<tr><th>Size</th><th>Name</th></tr>\n')
+        for index, fname in enumerate(sorted(os.listdir(dir))):
+            if index % 2 == 0:
+                bgcolor = '#D8D8D8'
+            else:
+                bgcolor = '#FFFFFF'
+            try:
+                size = str(os.path.getsize(os.path.join(dir, fname)))
+            except:
+                size = 'unknown'
+            link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
+            fh.write('<tr bgcolor="%s"><td>%s</td><td>%s</td></tr>\n' % (bgcolor, size, link))
+        fh.write('</table></body></html>\n')