python-pymzml 0.7.6-dfsg-1 / usr / lib / python2.7 / dist-packages / pymzml / run.py

# -*- coding: utf-8 -*-
# encoding: utf-8
"""
The class :py:class:`Reader` has been designed to selectively extract data
from a mzML file and to expose the data as a python object.
Necessary information are read in and stored in a fast
accessible format.
The reader itself is an iterator, thus looping over all spectra
follows the classical pythonian syntax.
Additionally one can random access spectra by their nativeID
if the file if not compressed or truncated by a conversion Program.

The class :py:class:`Writer` is still in development.

"""

# pymzml
#
# Copyright (C) 2010-2014 T. Bald, J. Barth, A. Niehues, M. Specht, H. Roest, C. Fufezan
#
#    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.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.

from __future__ import print_function

import sys
import re
import os
import bisect

from xml.etree import cElementTree

from collections import defaultdict as ddict

import pymzml.spec

import pymzml.obo
import pymzml.minimum


class RegexPatterns(object):
    spectrumIndexPattern = re.compile(
        b'(?P<type>(scan=|nativeID="))(?P<nativeID>[0-9]*)">(?P<offset>[0-9]*)</offset>'
    )
    simIndexPattern = re.compile(b'(?P<type>idRef=")(?P<nativeID>.*)">(?P<offset>[0-9]*)</offset>')


class Reader(object):
    """
    .. function:: __init__(
        path*
        [,noiseThreshold=0.0, extraAccessions=None, MS1_Precision=5e-6, MSn_Precision=20e-6]
    )

    Initializes an mzML run and returns an iterator.

    :param path: path to mzML file. File can be gzipped.
    :type path: string

    :param extraAccessions: list of additional (accession,fieldName) tuples.


        For example, ('MS:1000285',['value']) will extract the "total ion
        current" and store it under two keys in the spectrum, i.e.
        spectrum["total ion current"] or spectrum['MS:1000285'].

        The translated name is extracted from the current OBO file,
        hence the name that is defined by the HUPO-PSI consortium is used.
        (http://www.psidev.info/).

        pymzML comes with an example script queryOBO.py which can be used to
        lookup the names or MS tags (see: :py:obj:`queryOBO`).

        The value, i.e. which xml property has to be extraced has to be provided
        by the user. Multiple values can be used as input, i.e. ( 'MS:1000016' ,
        ['value','unitName'] ) will extract scan time and its unit.

    :type extraAccessions: list of tuples
    :param MS1_Precision: measured precision of MS1 spectra
    :type MS1_Precision: float
    :param MSn_Precision: measured precision of MSn spectra
    :type MSn_Precision: float
    :param build_index_from_scratch: build index from scratch
    :type build_index_from_scratch: boolean
    :param file_object: file object or any other iterable stream, this will make
                        path obsolete, seeking is disabled
    :type file_object: File_object like

    Example:

    >>> run = pymzml.run.Reader("../mzML_example_files/100729_t300_100729172744.mzML.gz",
                                MS1_Precision = 20e-6)
    """

    def __init__(
        self,
        path,
        noiseThreshold=0.0,
        extraAccessions=None,
        MS1_Precision=5e-6,
        MSn_Precision=20e-6,
        build_index_from_scratch=False,
        file_object=None,
        obo_version=None,
    ):
        # self.param contains user-specified parsing parameters
        self.param = dict()

        self.param['noiseThreshold'] = noiseThreshold
        self.param['MS1_Precision'] = MS1_Precision
        self.param['MSn_Precision'] = MSn_Precision
        self.param['accessions'] = {}

        # self.info contains information extracted from the mzML file
        self.info = dict()
        self.info['offsets'] = ddict()
        self.info['filename'] = path
        self.info['offsetList'] = []
        self.info['referenceableParamGroupList'] = False
        self.info['spectrum_count'] = 0
        self.info['obo_version'] = obo_version

        self.MS1_Precision = MS1_Precision

        self.elementList = []

        # Default stuff
        self.spectrum = pymzml.spec.Spectrum(
            measuredPrecision=MS1_Precision,
            param=self.param,
        )
        self.spectrum.clear()

        if file_object is not None:
            self.info['fileObject'] = file_object
            self.info['seekable'] = False
        else:
            if self.info['filename'].endswith('.gz'):
                import gzip
                import codecs
                self.info['fileObject'] = codecs.getreader("utf-8")(
                    gzip.open(self.info['filename'])
                )
                self.info['seekable'] = False
            else:
                self.info['fileObject'] = open(self.info['filename'], 'r')
                self.info['seekable'] = True

                # declare the seeker
                # read encoding ... maybe not really needed ...
                self.seeker = open(self.info['filename'], 'rb')
                header = self.seeker.readline()
                encodingPattern = re.compile(
                    b'encoding="(?P<encoding>[A-Za-z0-9-]*)"'
                )
                match = encodingPattern.search(header)
                if match:
                    self.info['encoding'] = bytes.decode(
                        match.group('encoding')
                    )
                else:
                    self.info['encoding'] = None

                # reading last 1024 bytes to find chromatogram Pos and SpectrumIndex Pos
                indexListOffsetPattern = re.compile(
                    b'<indexListOffset>(?P<indexListOffset>[0-9]*)</indexListOffset>'
                )
                chromatogramOffsetPattern = re.compile(
                    b'(?P<WTF>[nativeID|idRef])="TIC">(?P<offset>[0-9]*)</offset'
                )
                self.info['offsets']['indexList'] = None
                self.info['offsets']['TIC'] = None
                self.seeker.seek(0, 2)
                spectrumIndexPattern = RegexPatterns.spectrumIndexPattern
                for _ in range(10):  # max 10kbyte
                    # some converters fail in writing a correct index
                    # we found
                    # a) the offset is always the same (silent fail hurray!)
                    sanity_check_set = set()
                    try:
                        self.seeker.seek(-1024 * _, 1)
                    except:
                        break
                        # File is smaller than 10kbytes ...
                    for line in self.seeker:
                        match = chromatogramOffsetPattern.search(line)
                        if match:
                            self.info['offsets']['TIC'] = int(
                                bytes.decode(
                                    match.group('offset')
                                )
                            )

                        match_spec = spectrumIndexPattern.search(line)
                        if match_spec is not None:
                            spec_byte_offset = int(
                                bytes.decode(
                                    match_spec.group('offset')
                                )
                            )
                            sanity_check_set.add(spec_byte_offset)

                        match = indexListOffsetPattern.search(line)
                        if match:
                            self.info['offsets']['indexList'] = int(
                                bytes.decode(
                                    match.group('indexListOffset')
                                )
                            )
                            # break

                    if self.info['offsets']['indexList'] is not None and \
                            self.info['offsets']['TIC'] is not None:
                        break
                if len(sanity_check_set) <= 2:
                    # print( 'Convert error obvious ... ')
                    self.info['offsets']['indexList'] = None

                if self.info['offsets']['indexList'] is None:
                    # fall back to non-seekable
                    self.info['seekable'] = False
                    if build_index_from_scratch:
                        self._build_index_from_scratch(self.seeker)
                elif self.info['offsets']['TIC'] is not None and \
                        self.info['offsets']['TIC'] > os.path.getsize(self.info['filename']):
                    self.info['seekable'] = False
                else:
                    # Jumping to index list and slurpin all specOffsets
                    self.seeker.seek(self.info['offsets']['indexList'], 0)
                    spectrumIndexPattern = RegexPatterns.spectrumIndexPattern
                    simIndexPattern = RegexPatterns.simIndexPattern

                    # NOTE: this might be again different in another mzML versions!!
                    # 1.1 >> small_zlib.pwiz.1.1.mzML:
                    #   <offset idRef="controllerType=0 controllerNumber=1 scan=1">4363</offset>
                    # 1.0 >>
                    #   <offset idRef="S16004" nativeID="16004">236442042</offset>
                    #   <offset idRef="SIM SIC 651.5">330223452</offset>\n'
                    for line in self.seeker:
                        match_spec = spectrumIndexPattern.search(line)
                        if match_spec and match_spec.group('nativeID') == b'':
                            match_spec = None
                        match_sim = simIndexPattern.search(line)
                        if match_spec:
                            offset = int(bytes.decode(match_spec.group('offset')))
                            nativeID = int(bytes.decode(match_spec.group('nativeID')))
                            self.info['offsets'][nativeID] = offset
                            self.info['offsetList'].append(offset)
                        elif match_sim:
                            offset = int(bytes.decode(match_sim.group('offset')))
                            nativeID = bytes.decode(match_sim.group('nativeID'))
                            try:
                                nativeID = int( nativeID )
                            except:
                                pass
                            self.info['offsets'][nativeID] = offset
                            self.info['offsetList'].append(offset)
                    # opening seeker in normal mode again
                self.seeker.close()
                self.seeker = open(self.info['filename'], 'r')

        # declare the iter
        self.iter = iter(
            cElementTree.iterparse(
                self.info['fileObject'],
                events=(b'start', b'end')
            )
        )  # NOTE: end might be sufficient

        # Move iter to spectrumList / chromatogramList
        while True:
            event, element = next(self.iter)
            if element.tag.endswith('}mzML'):
                if 'version' in element.attrib and len(element.attrib['version']) > 0:
                    self.info['mzmlVersion'] = element.attrib['version']
                else:
                    s = element.attrib['{http://www.w3.org/2001/XMLSchema-instance}schemaLocation']
                    self.info['mzmlVersion'] = re.search(r'[0-9]*\.[0-9]*\.[0-9]*', s).group()
            elif element.tag.endswith('}cv'):
                if not self.info['obo_version'] and element.attrib['id'] == 'MS':
                    self.info['obo_version'] = element.attrib.get('version', '1.1.0')
                    # Really old convertions dont even have this this attribute
                    # wOooO?
            elif element.tag.endswith('}referenceableParamGroupList'):
                self.info['referenceableParamGroupList'] = True
                self.info['referenceableParamGroupListElement'] = element
            elif element.tag.endswith('}spectrumList'):
                self.info['spectrum_count'] = element.attrib['count']
                break
            elif element.tag.endswith('}chromatogramList'):
                # SRM only ?
                break
            else:
                pass
            # in any case:
            # build meta tree ...
            # self.meta.append( <> )

        # parse obo, check MS tags and if they are ok in minimum.py (minimum required) ...
        self.OT = pymzml.obo.oboTranslator(version=self.info['obo_version'])

        for minimumMS, ListOfvaluesToExtract in pymzml.minimum.MIN_REQ:
            self.param['accessions'][minimumMS] = {
                'valuesToExtract': ListOfvaluesToExtract,
                'name': self.OT[minimumMS],
                'values': []
            }

        # parse extra accessions ...
        if extraAccessions is not None:
            for accession, fieldIdentifiers in extraAccessions:
                if accession not in self.param['accessions'].keys():
                    self.param['accessions'][accession] = {
                        'valuesToExtract': [],
                        'name': self.OT[accession],
                        'values': []
                    }
                for valueToExtract in fieldIdentifiers:
                    if valueToExtract not in self.param['accessions'][accession]['valuesToExtract']:
                        self.param['accessions'][accession]['valuesToExtract'].append(
                            valueToExtract
                        )

        return

    def _build_index_from_scratch(self, seeker):
        """Build an index of spectra/chromatogram data with offsets by parsing the file."""

        def get_data_indices(fh, chunksize=8192, lookback_size=100):
            """Get a dictionary with binary file indices of spectra and
            chromatograms in an mzML file.

            Will parse quickly through the file and find all occurences of
            <chromatogram ... id="..." and <spectrum ... id="..." using a
            regex.
            We dont use an XML parser here because we need to know the
            exact location of the filepointer which is usually not possible
            with common xml parsers.
            """
            chrom_positions = {}
            spec_positions = {}
            chromcnt = 0
            speccnt = 0
            # regexes to be used
            chromexp = re.compile(b"<\s*chromatogram[^>]*id=\"([^\"]*)\"")
            chromcntexp = re.compile(b"<\s*chromatogramList\s*count=\"([^\"]*)\"")
            specexp = re.compile(b"<\s*spectrum[^>]*id=\"([^\"]*)\"")
            speccntexp = re.compile(b"<\s*spectrumList\s*count=\"([^\"]*)\"")
            # go to start of file
            fh.seek(0)
            prev_chunk = ""
            while True:
                 # read a chunk of data
                offset = fh.tell()
                chunk = fh.read(chunksize)
                if not chunk:
                    break

                 # append a part of the previous chunk since we have cut in the middle
                 # of the text (to make sure we dont miss anything, prev_chunk
                 # is analyzed twice).
                if len(prev_chunk) > 0:
                    chunk = prev_chunk[-lookback_size:] + chunk
                    offset -= lookback_size
                prev_chunk = chunk

                # find all occurences of the expressions and add to the dictionary
                for m in chromexp.finditer(chunk):
                    chrom_positions[m.group(1).decode('utf-8')] = offset + m.start()
                for m in specexp.finditer(chunk):
                    spec_positions[m.group(1).decode('utf-8')] = offset + m.start()
                m = chromcntexp.search(chunk)

                # also look for the total count of chromatograms and spectra
                # -> must be the same as the content of our dict!
                if m is not None:
                    chromcnt = int(m.group(1))
                m = speccntexp.search(chunk)
                if m is not None:
                    speccnt = int(m.group(1))

            # Check if everything is ok (e.g. we found the right number of
            # chromatograms and spectra) and then return the dictionary.
            if (chromcnt == len(chrom_positions) and speccnt == len(spec_positions)):
                positions = {}
                positions.update(chrom_positions)
                positions.update(spec_positions)
                # return positions # return only once in function leaves my brain sane :)

            else:
                positions = None
            return positions

        indices = get_data_indices(seeker)
        if indices is not None:
            self.info['offsets'].update(indices)
            self.info['offsetList'].extend(indices.values())

            # make sure the list is sorted (for bisect)
            self.info['offsetList'] = sorted(self.info['offsetList'])
            self.info['seekable'] = True
        return

    def __iter__(self):
        return self

    def __next__(self):
        """ The python 2.6+ iterator """
        return self.next()

    def next(self):
        """
        Iterator in class :py:class:`Run`:

        will return an instance of :py:class:`spec.Spectrum`, stored in run.spectrum.


        Example:

        >>> for spectrum in run:
        ...     print(spectrum['id'], end='\\r')

        """
        while True:
            event, element = next(self.iter, ('END', 'END'))
            # error? check cElementTree; conversion of data to 32bit-float mzml files might help
            # stop iteration when parsing is done
            if event == 'END':
                raise StopIteration

            if (
                (element.tag.endswith('}spectrum') or element.tag.endswith('}chromatogram'))
                and event == b'end'
            ):
                if self.info['referenceableParamGroupList']:
                    self.spectrum.initFromTreeObjectWithRef(
                        element,
                        self.info['referenceableParamGroupListElement']
                    )
                else:
                    self.spectrum.initFromTreeObject(element)

                try:
                    self.elementList[-1].clear()
                except:
                    pass

                self.elementList.append(element)

                return self.spectrum

    def __getitem__(self, value):
        '''
        Random access to spectra if mzML fill is indexed,
        not compressed and not truncted.

        Example:

        >>> spectrum_with_nativeID_100 = msrun[100]

        '''
        answer = None
        if self.info['seekable'] is True:
            if len(self.info['offsets']) == 0:
                print(
                    "File does support random access: index list missing...",
                    file=sys.stderr
                )

            if value in self.info['offsets']:
                startPos = self.info['offsets'][value]
                endPos_index = bisect.bisect_right(
                    self.info['offsetList'],
                    self.info['offsets'][value]
                )
                if endPos_index == len(self.info['offsetList']):
                    endPos = os.path.getsize(self.info['filename'])
                else:
                    endPos = self.info['offsetList'][endPos_index]

                self.seeker.seek(startPos, 0)
                data = self.seeker.read(endPos - self.info['offsets'][value])
                try:
                    self.spectrum.initFromTreeObject(cElementTree.fromstring(data))
                except:
                    # have closing </mzml> & </run> &or </spectrumList>
                    startingTag = data.split()[0]
                    stopIndex = data.index('</' + startingTag[1:] + '>')
                    self.spectrum.initFromTreeObject(
                        cElementTree.fromstring(data[:stopIndex + len(startingTag) + 2])
                    )
                answer = self.spectrum
            else:
                print("Run does not contain spec with native ID {0}".format(value), file=sys.stderr)
        else:
            self.iter = iter(cElementTree.iterparse(
                self.info['fileObject'],
                events=(b'start', b'end')
            ))  # NOTE: end might be sufficient

            for _ in self:
                if _['id'] == value:
                    answer = _
                    break
        return answer

    def getSpectrumCount(self):
        return self.info['spectrum_count']


class Writer(object):
    """
    .. function:: __init__(filename* ,run* [, overwrite = boolean])

    Initializes an mzML writer (beta stage).

    :param path: filename for the new mzML file.
    :type path: string
    :param run: Currently a pymzml.run.Reader object is required since we do
                not write the header by ourselves yet.
    :type run: pymzml.run.Reader
    :param overwrite: force the re-initialization of mzML file, even if file exists.
    :type overwrite: boolean

    Example:

    >>> run = pymzml.run.Reader(
    ...     '../mzML_example_files/100729_t300_100729172744.mzML',
    ...     MS1_Precision=5e-6,
    ... )
    >>> run2 = pymzml.run.Writer(filename='write_test.mzML', run=run , overwrite=True)
    >>> spec = run[1000]
    >>> run2.addSpec(spec)
    >>> run2.save()

    """
    def __init__(self, filename=None, run=None, overwrite=False):

        cElementTree.register_namespace("", "http://psi.hupo.org/ms/mzml")
        self.filename = filename
        self.lookup = {}

        self.newTree = None
        self.TreeBuilder = cElementTree.TreeBuilder()
        self.run = run
        self.info = {'counters': ddict(int)}

        if self.run.info['filename'].endswith('.gz'):
            import gzip
            import codecs
            io = codecs.getreader("utf-8")(gzip.open(self.run.info['filename']))
        else:
            io = open(self.run.info['filename'], 'r')

        for event, element in cElementTree.iterparse(io, events=(b'start', b'end')):
            if self.newTree is None:
                self.newTree = cElementTree.Element(element.tag, element.attrib)
                if event == b'start' and element.tag.endswith("}mzML"):
                    self.TreeBuilder.start(element.tag, element.attrib)
            else:
                if event == b'start':
                    self.TreeBuilder.start(element.tag, element.attrib)
                    if element.tag.endswith('}run'):
                        self.lookup['run'] = cElementTree.Element(element.tag, element.attrib)
                    if element.tag.endswith('}spectrumList'):
                        self.lookup['spectrumList'] = \
                            cElementTree.Element(element.tag, element.attrib)
                        self.lookup['spectrumIndeces'] = \
                            cElementTree.Element('index', {'name': 'spectrum'}),
                        break
                    elif element.tag.endswith('}chromatogramList'):
                        break
                    else:
                        pass
                else:
                    if element.tag.endswith('}softwareList'):
                        # Insert pymzML software tag
                        # Example:
                        #  <software id="pwiz_Reader_Thermo">
                        #  <softwareParam
                        #   accession="MS:1000615"
                        #   cvRef="MS"
                        #   name="ProteoWizard"
                        #   version="1.0"
                        #  />

                        self.TreeBuilder.start('software', {'id': 'pymzML 0.7.1'})
                        self.TreeBuilder.start('softwareParam', {
                            'accession': 'MS:0000000',
                            'cvRef': 'MS',
                            'name': 'pymzML writer',
                            'version': '0.7.1',
                        })
                        self.newTree.append(self.TreeBuilder.end('softwareParam'))
                        self.newTree.append(self.TreeBuilder.end('software'))
                    self.TreeBuilder.data(element.text)
                    self.newTree.append(self.TreeBuilder.end(element.tag))
        return

    def addSpec(self, spec):
        self._addTree(spec, typeOfSpec='spectrum')
        return

    def addChromatogram(self, spec):
        self._addTree(spec, typeOfSpec='chromatogram')
        return

    def _addTree(self, spec, typeOfSpec=None):
        if typeOfSpec not in self.lookup.keys():
            self.lookup['{0}List'.format(typeOfSpec)] = \
                cElementTree.Element('{0}List'.format(typeOfSpec), {'count': 0})
            self.lookup['{0}Indeces'.format(typeOfSpec)] = \
                cElementTree.Element('index', {'name': typeOfSpec})

        self.lookup[typeOfSpec + 'List'].append(spec._xmlTree)
        offset = cElementTree.Element('offset')
        offset.text = 'Not implemented yet'
        offset.attrib = {'idRef': 'NaN', 'nativeID': str(spec['id'])}
        self.lookup[typeOfSpec + 'Indeces'].append(offset)

        self.info['counters'][typeOfSpec] += 1

        return

    def save(self):
        for typeOfSpec in ['spectrum', 'chromatogram']:
            if typeOfSpec + 'List' in self.lookup.keys():
                self.lookup['{0}List'.format(typeOfSpec)].set(
                    'count', str(self.info['counters'][typeOfSpec]),
                )
                self.lookup['run'].append(self.lookup[typeOfSpec + 'List'])
        self.newTree.append(self.lookup['run'])

        IndexList = cElementTree.Element('IndexList', {
            'count': str(len(self.info['counters'].keys()))
        })

        for typeOfSpec in ['spectrum', 'chromatogram']:
            if typeOfSpec + 'Indeces' in self.lookup.keys():
                IndexList.append(self.lookup['{0}Indeces'.format(typeOfSpec)])
        self.newTree.append(IndexList)

        self.prettyXMLformater(self.newTree)
        self.xmlTree = cElementTree.ElementTree(self.newTree)
        self.xmlTree.write(self.filename, encoding='ISO-8859-1', xml_declaration=True)

        return

    def prettyXMLformater(self, element, level=0):
        # Modified version from
        # http://infix.se/2007/02/06/gentlemen-indent-your-xml
        # which is a modified version of
        # http://effbot.org/zone/element-lib.htm#prettyprint

        i = '\n{0}'.format(level * ' ')
        if len(element):
            if not element.text or not element.text.strip():
                element.text = i + '  '
            for e in element:
                self.prettyXMLformater(e, level + 1)
                if not e.tail or not e.tail.strip():
                    e.tail = i + '  '
            if not e.tail or not e.tail.strip():
                e.tail = i
        else:
            if level and (not element.tail or not element.tail.strip()):
                element.tail = i
        return


if __name__ == '__main__':
    print(__doc__)