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# -------------------------------------------------------------------------
# Copyright (C) 2005-2012 Martin Strohalm <www.mmass.org>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load libs
import os.path
# load stopper
from mod_stopper import CHECK_FORCE_QUIT
# load parsers
from parser_xy import parseXY
from parser_mzxml import parseMZXML
from parser_mzdata import parseMZDATA
from parser_mzml import parseMZML
from parser_mgf import parseMGF
from parser_fasta import parseFASTA
# UTILITIES
# ---------
def load(path, scanID=None, dataType='continuous'):
"""Load scan from given document."""
# check path
if not os.path.exists(path):
raise IOError, 'File not found! --> ' + path
# get filename and extension
dirName, fileName = os.path.split(path)
baseName, extension = os.path.splitext(fileName)
fileName = fileName.lower()
baseName = baseName.lower()
extension = extension.lower()
# get document type
if extension == '.mzdata':
docType = 'mzData'
elif extension == '.mzxml':
docType = 'mzXML'
elif extension == '.mzml':
docType = 'mzML'
elif extension == '.mgf':
docType = 'MGF'
elif extension in ('.xy', '.txt', '.asc'):
docType = 'XY'
elif extension == '.xml':
doc = open(path, 'r')
data = doc.read(500)
if '<mzData' in data:
docType = 'mzData'
elif '<mzXML' in data:
docType = 'mzXML'
elif '<mzML' in data:
docType = 'mzML'
doc.close()
# check document type
if not docType:
raise ValueError, 'Unknown document type! --> ' + path
# load document data
if docType == 'mzData':
parser = parseMZDATA(path)
scan = parser.scan(scanID)
elif docType == 'mzXML':
parser = parseMZXML(path)
scan = parser.scan(scanID)
elif docType == 'mzML':
parser = parseMZML(path)
scan = parser.scan(scanID)
elif docType == 'MGF':
parser = parseMGF(path)
scan = parser.scan(scanID)
elif docType == 'XY':
parser = parseXY(path)
scan = parser.scan(dataType)
return scan
# ----
def save(data, path):
""""""
buff = ''
for point in data:
buff += "%f\t%f\n" % tuple(point)
save = file(path, 'w')
save.write(buff.encode("utf-8"))
save.close()
# ----
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