annotate ms_data_converter.py @ 0:dfafbfd7983d

Uploaded

1 #!/usr/bin/env python
2 import optparse
3 import os
4 import sys
5 import tempfile
6 import shutil
7 import subprocess
8 import re
9 import logging
10 
11 assert sys.version_info[:2] >= (2, 6)
12 
13 log = logging.getLogger(__name__)
14 working_directory = os.getcwd()
15 tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name
16 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name
17 
18 
19 def stop_err(msg):
20     sys.stderr.write("%s\n" % msg)
21     sys.exit()
22 
23 
24 def read_stderr():
25     stderr = ''
26     if(os.path.exists(tmp_stderr_name)):
27         with open(tmp_stderr_name, 'rb') as tmp_stderr:
28             buffsize = 1048576
29             try:
30                 while True:
31                     stderr += tmp_stderr.read(buffsize)
32                     if not stderr or len(stderr) % buffsize != 0:
33                         break
34             except OverflowError:
35                 pass
36     return stderr
37 
38 
39 def execute(command, stdin=None):
40     try:
41         with open(tmp_stderr_name, 'wb') as tmp_stderr:
42             with open(tmp_stdout_name, 'wb') as tmp_stdout:
43                 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
44                 returncode = proc.wait()
45                 if returncode != 0:
46                     raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
47     finally:
48         print(( open(tmp_stderr_name, "r").read() ))
49         print(( open(tmp_stdout_name, "r").read() ))
50 
51 
52 def delete_file(path):
53     if os.path.exists(path):
54         try:
55             os.remove(path)
56         except:
57             pass
58 
59 
60 def delete_directory(directory):
61     if os.path.exists(directory):
62         try:
63             shutil.rmtree(directory)
64         except:
65             pass
66 
67 
68 def symlink(source, link_name):
69     import platform
70     if platform.system() == 'Windows':
71         try:
72             import win32file
73             win32file.CreateSymbolicLink(source, link_name, 1)
74         except:
75             shutil.copy(source, link_name)
76     else:
77         os.symlink(source, link_name)
78 
79 
80 def copy_to_working_directory(data_file, relative_path):
81     if os.path.abspath(data_file) != os.path.abspath(relative_path):
82         symlink(data_file, relative_path)
83     return relative_path
84 
85 
86 def __main__():
87     run_script()
88 
89 #ENDTEMPLATE
90 
91 def str_to_bool(v):
92     """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
93     return v.lower() in ["yes", "true", "t", "1"]
94 
95 def shellquote(s):
96     return '"' + s.replace('"', '\\"') + '"'
97 
98 def run_script():
99     parser = optparse.OptionParser()
00     parser.add_option('--input', dest='inputs', action='append', default=[])
01     parser.add_option('--input_name', dest='input_names', action='append', default=[])
02     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.')
03     parser.add_option('--output', dest='output')
04     parser.add_option('--fromextension', dest='fromextension')
05     parser.add_option('--toextension', dest='toextension', default='mzML', choices=['mzML', 'mgf'])
06     parser.add_option('--content_type', dest='content_type', default='centroid', choices=['profile', 'centroid', 'proteinpilot'])
07     parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
08     parser.add_option('--zlib', dest='zlib', default="false")
09     parser.add_option('--index', dest='index', default="false")
10     parser.add_option('--debug', dest='debug', action='store_true', default=False)
11 
12     (options, args) = parser.parse_args()
13     if len(options.inputs) < 1:
14         stop_err("No input files to ms_data_convert specified")
15     if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):
16         stop_err("Number(s) of supplied input names and input files do not match")
17     if not options.output:
18         stop_err("Must specify output location")
19     input_files = []
20     for i, input in enumerate(options.inputs):
21         input_base = None
22         if len(options.input_names) > i:
23             input_base = options.input_names[i]
24             input_base = input_base.replace("'", "").replace("\"", "")
25             print("1- input_base: %s" % input_base)
26         if not input_base:
27             input_base = 'input%s' % i
28             print("2- input_base: %s" % input_base)
29         if not input_base.lower().endswith(options.fromextension.lower()) and input not in options.implicits:
30             input_file = '%s.%s' % (input_base, options.fromextension)
31             print("3- input_base: %s" % input_base)
32             print("3- input_file: %s" % input_file)
33         else:
34             input_file = input_base
35             print("4- input_base: %s" % input_base)
36             print("4- input_file: %s" % input_file)
37         input_file = input_file
38         copy_to_working_directory(input, input_file)
39         if input not in options.implicits:
40             input_files.append(input_file)
41     ## AB_SCIEX_MS_Converter <input format> <input data> <output content type> <output format> <output file> [data compression setting] [data precision setting] [create index flag]
42     inputs_as_str = " ".join(['%s' % shellquote(input) for input in input_files])
43     output_file = re.sub('(%s)?$' % options.fromextension.lower(), options.toextension, input_files[0].lower())
44     cmd = "AB_SCIEX_MS_Converter %s %s %s %s %s" % (options.fromextension.upper(), inputs_as_str, options.content_type, options.toextension.upper(), output_file )
45     if str_to_bool(options.zlib):
46         cmd = "%s %s" % (cmd, "/zlib")
47     if options.binaryencoding:
48         cmd = "%s %s" % (cmd, "/singleprecision" if options.binaryencoding == '32' else "/doubleprecision")
49     if str_to_bool(options.zlib):
50         cmd = "%s %s" % (cmd, "/index")
51     if options.debug:
52         print(cmd)
53     execute(cmd)
54     shutil.copy(output_file, options.output)
55 
56 if __name__ == '__main__':
57     __main__()