annotate protxml2html_wrapper.py @ 0:156ef965340e draft default tip

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#!/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):
    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.set_defaults(export_spreadsheet=False)
    (options, args) = parser.parse_args()

    copy_to_working_directory(options.input, "input.prot.xml")
    # Trans-Proteomic Pipeline - bin/protxml2html.pl
    cmd = "protxml2html.pl -file ./input.prot.xml"
    if options.export_spreadsheet:
        cmd = "%s FORMAT EXCEL" % cmd
    else:
        cmd = "%s FORMAT HTML" % cmd
    execute(cmd)

if __name__ == '__main__': __main__()