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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# --------------------------------------------------------------------------
# OpenMS -- Open-Source Mass Spectrometry
# --------------------------------------------------------------------------
# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
# ETH Zurich, and Freie Universitaet Berlin 2002-2018.
# This software is released under a three-clause BSD license:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of any author or any participating institution
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
# For a full list of authors, refer to the file AUTHORS.
# --------------------------------------------------------------------------
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# --------------------------------------------------------------------------
# $Maintainer: Hendrik Weisser $
# $Authors: Hendrik Weisser $
# --------------------------------------------------------------------------
"""Convert featureXML files between formats used before and after OpenMS 1.8"""
import sys
import re
import os.path
if len(sys.argv) < 3:
sys.exit("Error: two parameters (input featureXML, output featureXML) "
"expected!")
in_path = sys.argv[1]
out_path = sys.argv[2]
if os.path.realpath(in_path) == os.path.realpath(out_path):
sys.exit("Error: output path must be different from input path!")
old_pattern = re.compile('<hullpoint>\n<hposition dim="0">(.*)</hposition>\n'
'<hposition dim="1">(.*)</hposition>\n</hullpoint>')
new_pattern = re.compile('<pt x="(.*)" y="(.*)" */>')
with open(in_path) as source:
with open(out_path, "w") as sink:
line_count = 0
for line in source:
line_count += 1
stripped = line.strip()
if stripped == "<hullpoint>": # convert old to new:
temp_count = line_count
indent = line[:line.index("<")]
content = stripped
while stripped != "</hullpoint>":
stripped = source.next().strip()
line_count += 1
content += "\n" + stripped
match = old_pattern.match(content)
if not match:
print "skipping unexpected content in lines %d-%d" % \
(temp_count, line_count)
else:
sink.write(indent + '<pt x="%s" y="%s" />\n' %
(match.group(1), match.group(2)))
continue
# else:
match = new_pattern.match(stripped)
if match: # convert new to old:
indent = line[:line.index("<")]
sink.write(indent + "<hullpoint>\n")
sink.write(indent + '\t<hposition dim="0">%s</hposition>\n' %
match.group(1))
sink.write(indent + '\t<hposition dim="1">%s</hposition>\n' %
match.group(2))
sink.write(indent + "</hullpoint>\n")
else:
sink.write(line)
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