--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/pepxml_viewer_wrapper.py	Wed Oct 08 13:49:16 2014 -0400
@@ -0,0 +1,137 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import subprocess
+import shutil
+import logging
+
+assert sys.version_info[:2] >= ( 2, 6 )
+
+log = logging.getLogger(__name__)
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
+
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+    return stderr
+
+
+def execute(command, stdin=None):
+    with open(tmp_stderr_name, 'wb') as tmp_stderr:
+        with open(tmp_stdout_name, 'wb') as tmp_stdout:
+            proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
+            returncode = proc.wait()
+            if returncode != 0:
+                raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
+
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        import win32file
+        win32file.CreateSymbolicLink(source, link_name, 1)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        shutil.copy(data_file, relative_path)
+    return relative_path
+
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option("--input")
+    parser.add_option("--export_spreadsheet", action="store_true", dest="export_spreadsheet")
+    parser.add_option("--append_unmodified_peptide", action="store_true", dest="append_unmodified_peptide", default=False)
+    parser.set_defaults(export_spreadsheet=False)
+    (options, args) = parser.parse_args()
+
+    copy_to_working_directory(options.input, "input.pep.xml")
+    # Trans-Proteomic Pipeline - cgi-bin/PepXMLViewer.cgi
+    cmd = "PepXMLViewer.cgi -I input.pep.xml"
+    cmd = "%s %s" % (cmd, "-B exportSpreadsheet")
+    if options.export_spreadsheet:
+        cmd = "%s %s" % (cmd, "1")
+    else:
+        cmd = "%s %s" % (cmd, "0")
+    execute(cmd)
+    if options.append_unmodified_peptide:
+        from csv import reader
+        csv_opts = {'delimiter': '\t'}
+        first = True
+        with open("tmp.xls", "w") as output:
+            peptide_index = None
+            for row in reader(open("input.pep.xls", "r"), **csv_opts):
+                if first:
+                    peptide_index = row.index("peptide")
+                    row.append("unmodified_peptide")
+                    output.write("\t".join(row))
+                    output.write("\n")
+                    first = False
+                else:
+                    row.append(unmodify(row[peptide_index]))
+                    output.write("\t".join(row))
+                    output.write("\n")
+        execute("mv tmp.xls input.pep.xls")
+
+
+def unmodify(peptide):
+    """
+
+    >>> from re import sub
+    >>> sub(r'\[(\-|\d|\.)+\]', '', 'A[-12.34]B')
+    'AB'
+    """
+    from re import sub
+    peptide = sub(r'\[(\-|\d|\.)+\]', '', peptide)
+    peptide = sub(r'^.\.|\..$|n|c', '', peptide)
+    #peptide = sub(r'\..$', '', peptide)
+    #peptide = sub(r'\[.+\]', '', peptide)
+    return peptide
+
+
+if __name__ == '__main__':
+    __main__()