Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder

diff utils.py @ 0:7000422fbaff draft

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author greg
date Thu, 08 Jun 2017 12:51:58 -0400
parents
children a7867769a706
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.py	Thu Jun 08 12:51:58 2017 -0400
@@ -0,0 +1,80 @@
+import os
+import shutil
+import subprocess
+import sys
+
+FSTDERR = 'stderr.txt'
+FSTDOUT = 'stdout.txt'
+
+
+def check_execution_errors(rc, fstderr, fstdout):
+    if rc != 0:
+        fh = open(fstdout, 'rb')
+        out_msg = fh.read()
+        fh.close()
+        fh = open(fstderr, 'rb')
+        err_msg = fh.read()
+        fh.close()
+        msg = '%s\n%s\n' % (str(out_msg), str(err_msg))
+        stop_err(msg)
+
+
+def get_response_buffers():
+    fstderr = os.path.join(os.getcwd(), FSTDERR)
+    fherr = open(fstderr, 'wb')
+    fstdout = os.path.join(os.getcwd(), FSTDOUT)
+    fhout = open(fstdout, 'wb')
+    return fstderr, fherr, fstdout, fhout
+
+
+def move_directory_files(source_dir, destination_dir, copy=False):
+    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)
+        if copy:
+            shutil.copy(source_entry, destination_directory)
+        else:
+            shutil.move(source_entry, destination_directory)
+
+
+def run_command(cmd):
+    fstderr, fherr, fstdout, fhout = get_response_buffers()
+    proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True)
+    rc = proc.wait()
+    # Check results.
+    fherr.close()
+    fhout.close()
+    check_execution_errors(rc, fstderr, fstdout)
+
+
+def stop_err(msg):
+    sys.exit(msg)
+
+
+def write_html_output(output, title, dir):
+    with open(output, 'w') as fh:
+        dir_items = sorted(os.listdir(dir))
+        # Directories can only contain either files or directories,
+        # but not both.
+        if len(dir_items) > 0:
+            item_path = os.path.join(dir, dir_items[0])
+            if os.path.isdir(item_path):
+                header = 'Directories'
+            else:
+                header = 'Datasets'
+        else:
+            header = ''
+        fh.write('<html><head><h3>%s: %d items</h3></head>\n' % (title, len(dir_items)))
+        fh.write('<body><p/><table cellpadding="2">\n')
+        fh.write('<tr><b>%s</th></b>\n' % header)
+        for index, fname in enumerate(dir_items):
+            if index % 2 == 0:
+                bgcolor = '#D8D8D8'
+            else:
+                bgcolor = '#FFFFFF'
+            link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
+            fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, link))
+        fh.write('</table></body></html>\n')