# HG changeset patch
# User galaxyp
# Date 1426088186 14400
# Node ID dfafbfd7983d3467b55457182cc56ae3b7eff3e7
Uploaded
diff -r 000000000000 -r dfafbfd7983d ms_data_converter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ms_data_converter.py Wed Mar 11 11:36:26 2015 -0400
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil
+import subprocess
+import re
+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):
+ try:
+ 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()))
+ finally:
+ print(( open(tmp_stderr_name, "r").read() ))
+ print(( open(tmp_stdout_name, "r").read() ))
+
+
+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':
+ try:
+ import win32file
+ win32file.CreateSymbolicLink(source, link_name, 1)
+ except:
+ shutil.copy(source, link_name)
+ 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):
+ symlink(data_file, relative_path)
+ return relative_path
+
+
+def __main__():
+ run_script()
+
+#ENDTEMPLATE
+
+def str_to_bool(v):
+ """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
+ return v.lower() in ["yes", "true", "t", "1"]
+
+def shellquote(s):
+ return '"' + s.replace('"', '\\"') + '"'
+
+def run_script():
+ parser = optparse.OptionParser()
+ parser.add_option('--input', dest='inputs', action='append', default=[])
+ parser.add_option('--input_name', dest='input_names', action='append', default=[])
+ parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the AB SCIEX MS Data Converter command line.')
+ parser.add_option('--output', dest='output')
+ parser.add_option('--fromextension', dest='fromextension')
+ parser.add_option('--toextension', dest='toextension', default='mzML', choices=['mzML', 'mgf'])
+ parser.add_option('--content_type', dest='content_type', default='centroid', choices=['profile', 'centroid', 'proteinpilot'])
+ parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+ parser.add_option('--zlib', dest='zlib', default="false")
+ parser.add_option('--index', dest='index', default="false")
+ parser.add_option('--debug', dest='debug', action='store_true', default=False)
+
+ (options, args) = parser.parse_args()
+ if len(options.inputs) < 1:
+ stop_err("No input files to ms_data_convert specified")
+ if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
+ stop_err("Number(s) of supplied input names and input files do not match")
+ if not options.output:
+ stop_err("Must specify output location")
+ input_files = []
+ for i, input in enumerate(options.inputs):
+ input_base = None
+ if len(options.input_names) > i:
+ input_base = options.input_names[i]
+ input_base = input_base.replace("'", "").replace("\"", "")
+ print("1- input_base: %s" % input_base)
+ if not input_base:
+ input_base = 'input%s' % i
+ print("2- input_base: %s" % input_base)
+ if not input_base.lower().endswith(options.fromextension.lower()) and input not in options.implicits:
+ input_file = '%s.%s' % (input_base, options.fromextension)
+ print("3- input_base: %s" % input_base)
+ print("3- input_file: %s" % input_file)
+ else:
+ input_file = input_base
+ print("4- input_base: %s" % input_base)
+ print("4- input_file: %s" % input_file)
+ input_file = input_file
+ copy_to_working_directory(input, input_file)
+ if input not in options.implicits:
+ input_files.append(input_file)
+ ## AB_SCIEX_MS_Converter