diff galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_wrapper.py @ 0:942cec8d04c7 draft

Initial commit.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxyp-galaxyp-toolshed-msconvert-9663ae998499/msconvert_wrapper.py	Wed Sep 19 00:07:16 2012 -0400
@@ -0,0 +1,182 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil 
+import subprocess
+import re
+from os.path import basename
+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':
+        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
+
+to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2']
+
+
+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 _add_filter(filters_file, contents):
+    filters_file.write("filter=\"%s\"\n" % contents)
+
+
+def _read_table_numbers(path):
+    unique_numbers = set([])
+    input = open(path, "r")
+    first_line = True
+    for line in input:
+        if not line:
+            continue
+        line = line.strip()
+        if line.startswith("#"):
+            first_line = False
+            continue
+        match = re.match("\d+", line)
+        if match:
+            unique_numbers.add(int(match.group()))
+        first_line = False
+    return unique_numbers
+
+
+def _add_filter_line_from_file(file, filter_file, filter_prefix):
+    if not file:
+        return
+    numbers = _read_table_numbers(file)
+    msconvert_int_set = " ".join([str(number) for number in numbers])
+    _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set))
+
+
+def _create_filters_file(options):
+    filters_file_path = "filters"
+    filters_file = open(filters_file_path, "w")
+    if options.filters_file:
+        filters_file.write(open(options.filters_file, "r").read())
+    for filter in options.filter:
+        _add_filter(filters_file, filter)
+    _add_filter_line_from_file(options.filter_indices_table, filters_file, "index")
+    _add_filter_line_from_file(options.filter_numbers_table, filters_file, "scanNumber")
+
+    filters_file.close()
+    print open(filters_file_path, "r").read()
+    return filters_file_path
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option('--input', dest='input')
+    parser.add_option('--output', dest='output')
+    parser.add_option('--fromextension', dest='fromextension')
+    parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
+    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
+    parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
+    parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])
+    parser.add_option('--zlib', dest='zlib', default="false")
+    parser.add_option('--filter', dest='filter', action='append', default=[])
+    parser.add_option('--filters_file', dest='filters_file', default=None)
+    parser.add_option('--filter_indices_table', default=None)
+    parser.add_option('--filter_numbers_table', default=None)
+
+    (options, args) = parser.parse_args()
+
+    input_file = 'input.%s' % options.fromextension
+    copy_to_working_directory(options.input, input_file)
+    os.mkdir('output')
+    to_extension = options.toextension
+    if to_extension.startswith("unindexed_"):
+        to_extension = to_extension[len("unindexed_"):]
+        to_params = "--noindex"
+    else:
+        to_params = ""
+    cmd = "msconvert --%s %s -o output" % (to_extension, to_params)
+    if str_to_bool(options.zlib):
+        cmd = "%s %s" % (cmd, "--zlib")
+    if options.binaryencoding:
+        cmd = "%s --%s" % (cmd, options.binaryencoding)
+    if options.mzencoding:
+        cmd = "%s --mz%s" % (cmd, options.mzencoding)
+    if options.intensityencoding:
+        cmd = "%s --inten%s" % (cmd, options.intensityencoding)
+    cmd = "%s %s" % (cmd, input_file)
+    filters_file_path = _create_filters_file(options)
+    cmd = "%s -c %s" % (cmd, filters_file_path)
+    print cmd
+    execute(cmd)
+    output_files = os.listdir('output')
+    assert len(output_files) == 1
+    output_file = output_files[0]
+    shutil.copy(os.path.join('output', output_file), options.output)
+
+
+if __name__ == '__main__': __main__()