comparison proteomics.py @ 3:b22ebbb05260 draft

Uploaded

2:7edcae695986

"""
Proteomics format classes
"""
import logging
import re
from galaxy.datatypes.data import *
from galaxy.datatypes.xml import *
from galaxy.datatypes.sniff import *
from galaxy.datatypes.binary import *
from galaxy.datatypes.interval import *

log = logging.getLogger(__name__)

class ProtGff( Gff ):
    """Tab delimited data in Gff format"""
    file_ext = "prot_gff"
    def set_peek( self, dataset, is_multi_byte=False ):
        """Set the peek and blurb text"""
        if not dataset.dataset.purged:
            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
            dataset.blurb = 'Proteogenomics GFF'
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        handle = open(filename)
        xmlns_re = re.compile("^##gff-version")
        for i in range(3):
            line = handle.readline()
            if xmlns_re.match(line.strip()):
                handle.close()
                return True

        handle.close()
        return False


class Xls( Binary ):
    """Class describing a binary excel spreadsheet file"""
    file_ext = "xls"

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
            dataset.peek  = "Excel Spreadsheet file"
            dataset.blurb = data.nice_size( dataset.get_size() )
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'
    def display_peek( self, dataset ):
        try:
            return dataset.peek
        except:
            return "Binary xls file (%s)" % ( data.nice_size( dataset.get_size() ) )

class ProteomicsXml(GenericXml):
    """ An enhanced XML datatype used to reuse code across several
    proteomic/mass-spec datatypes. """

    def sniff(self, filename):
        """ Determines whether the file is the correct XML type. """
        with open(filename, 'r') as contents:            
            while True:
                line = contents.readline()
                if line == None or not line.startswith('<?'):
                    break
            pattern = '^<(\w*:)?%s' % self.root # pattern match <root or <ns:root for any ns string

            dataset.blurb = self.blurb
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

class PepXml(ProteomicsXml):
    """pepXML data"""
    file_ext = "pepxml"
    blurb = 'pepXML data'
    root = "msms_pipeline_analysis"
    

class MzML(ProteomicsXml):
    """mzML data"""
    file_ext = "mzml"
    blurb = 'mzML Mass Spectrometry data'

    root = "protein_summary"


class MzXML(ProteomicsXml):
    """mzXML data"""
    file_ext = "mzXML"
    blurb = "mzXML Mass Spectrometry data"
    root = "mzXML"

## PSI datatypes
class MzIdentML(ProteomicsXml):
    file_ext = "mzid"
    blurb = "XML identified peptides and proteins."
    root = "MzIdentML"
    

class TraML(ProteomicsXml):
    file_ext = "traML"
    blurb = "TraML transition list"
    root = "TraML"


class MzQuantML(ProteomicsXml):
    file_ext = "mzq"
    blurb = "XML quantification data"
    root = "MzQuantML"

 
class Mgf( Text ):
    """Mascot Generic Format data"""
    file_ext = "mgf"

    def set_peek( self, dataset, is_multi_byte=False ):

            dataset.blurb = 'mgf Mascot Generic Format'
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'


    def sniff( self, filename ):
        mgf_begin_ions = "BEGIN IONS"
        max_lines=100

        for i, line in enumerate( file( filename ) ):
            line = line.rstrip( '\n\r' )
            if line==mgf_begin_ions:
                return True
            if i>max_lines:
                return False
            
                
class MascotDat( Text ):
    """Mascot search results """
    file_ext = "mascotdat"

    def set_peek( self, dataset, is_multi_byte=False ):

        except:
            return "Thermo Finnigan RAW file (%s)" % ( data.nice_size( dataset.get_size() ) )


if hasattr(Binary, 'register_sniffable_binary_format'):
    Binary.register_sniffable_binary_format('RAW', 'RAW', RAW)


class Msp(Text):
    """ Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf """
    file_ext = "msp"
    
    @staticmethod
    def next_line_starts_with(contents, prefix):

                return False

        return True

# unsniffable binary format, should do something about this
class XHunterAslFormat(Binary):
    """ Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html """
    file_ext = "hlf"


if hasattr(Binary, 'register_unsniffable_binary_ext'):
    Binary.register_unsniffable_binary_ext('hlf')

3:b22ebbb05260

"""
Proteomics format classes
"""
import logging
import re
import binascii

from galaxy.datatypes.sniff import *
from galaxy.datatypes import data
from galaxy.datatypes.data import Text
from galaxy.datatypes.xml import GenericXml
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.tabular import Tabular
from galaxy.datatypes.interval import Gff

log = logging.getLogger(__name__)


class Wiff( Binary ):
    """Class for wiff files."""
    file_ext = 'wiff'
    allow_datatype_change = False
    composite_type = 'auto_primary_file'

    def __init__(self, **kwd):
        Binary.__init__(self, **kwd)
        self.add_composite_file( 'wiff', 
            description = 'AB SCIEX files in .wiff format. This can contain all needed information or only metadata.', 
            is_binary = True )
        self.add_composite_file( 'wiff_scan', 
            description = 'AB SCIEX spectra file (wiff.scan), if the corresponding .wiff file only contains metadata.', 
            optional = 'True', is_binary = True )

    def generate_primary_file( self, dataset = None ):
        rval = ['<html><head><title>Wiff Composite Dataset </title></head><p/>']
        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
            fn = composite_name
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
            if composite_file.get('description'):
                rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
            else:
                rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
        rval.append( '</ul></div></html>' )
        return "\n".join( rval )



if hasattr(Binary, 'register_unsniffable_binary_ext'):
    Binary.register_unsniffable_binary_ext('wiff')


class IdpDB( Binary ):
    file_ext = "idpDB"

if hasattr(Binary, 'register_unsniffable_binary_ext'):
    Binary.register_unsniffable_binary_ext('idpDB')


class PepXmlReport( Tabular ):
    """pepxml converted to tabular report"""
    file_ext = "tsv"

    def __init__(self, **kwd):
        Tabular.__init__( self, **kwd )
        self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probabaility']

    def display_peek( self, dataset ):
        """Returns formated html of peek"""
        return Tabular.make_html_table( self, dataset, column_names=self.column_names )


class ProtXmlReport( Tabular ):
    """protxml converted to tabular report"""
    file_ext = "tsv"
    comment_lines = 1
    
    def __init__(self, **kwd):
        Tabular.__init__( self, **kwd )
        self.column_names = ["Entry Number", "Group Probability", "Protein", "Protein Link", "Protein Probability", "Percent Coverage", "Number of Unique Peptides", "Total Independent Spectra", "Percent Share of Spectrum ID's", "Description", "Protein Molecular Weight", "Protein Length", "Is Nondegenerate Evidence", "Weight", "Precursor Ion Charge", "Peptide sequence", "Peptide Link", "NSP Adjusted Probability", "Initial Probability", "Number of Total Termini", "Number of Sibling Peptides Bin", "Number of Instances", "Peptide Group Designator", "Is Evidence?"]

    def display_peek( self, dataset ):
        """Returns formated html of peek"""
        return Tabular.make_html_table( self, dataset, column_names=self.column_names )

class ProteomicsXml( GenericXml ):
    """ An enhanced XML datatype used to reuse code across several
    proteomic/mass-spec datatypes. """

    def sniff(self, filename):
        """ Determines whether the file is the correct XML type. """
        with open(filename, 'r') as contents:
            while True:
                line = contents.readline()
                if line == None or not line.startswith('<?'):
                    break
            pattern = '^<(\w*:)?%s' % self.root # pattern match <root or <ns:root for any ns string

            dataset.blurb = self.blurb
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'


class PepXml(ProteomicsXml):
    """pepXML data"""
    file_ext = "pepxml"
    blurb = 'pepXML data'
    root = "msms_pipeline_analysis"


class MzML(ProteomicsXml):
    """mzML data"""
    file_ext = "mzml"
    blurb = 'mzML Mass Spectrometry data'

    root = "protein_summary"


class MzXML(ProteomicsXml):
    """mzXML data"""
    file_ext = "mzxml"
    blurb = "mzXML Mass Spectrometry data"
    root = "mzXML"

## PSI datatypes
class MzIdentML(ProteomicsXml):
    file_ext = "mzid"
    blurb = "XML identified peptides and proteins."
    root = "MzIdentML"


class TraML(ProteomicsXml):
    file_ext = "traml"
    blurb = "TraML transition list"
    root = "TraML"


class MzQuantML(ProteomicsXml):
    file_ext = "mzq"
    blurb = "XML quantification data"
    root = "MzQuantML"


class ConsensusXML(ProteomicsXml):
    file_ext = "consensusxml"
    blurb = "OpenMS multiple LC-MS map alignment file"
    root = "consensusXML"


class FeatureXML(ProteomicsXml):
    file_ext = "featurexml"
    blurb = "OpenMS feature file"
    root = "featureMap"


class IdXML(ProteomicsXml):
    file_ext = "idxml"
    blurb = "OpenMS identification file"
    root = "IdXML"


class Mgf( Text ):
    """Mascot Generic Format data"""
    file_ext = "mgf"

    def set_peek( self, dataset, is_multi_byte=False ):

            dataset.blurb = 'mgf Mascot Generic Format'
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def sniff( self, filename ):
        mgf_begin_ions = "BEGIN IONS"
        max_lines=100

        for i, line in enumerate( file( filename ) ):
            line = line.rstrip( '\n\r' )
            if line==mgf_begin_ions:
                return True
            if i>max_lines:
                return False


class MascotDat( Text ):
    """Mascot search results """
    file_ext = "mascotdat"

    def set_peek( self, dataset, is_multi_byte=False ):

        except:
            return "Thermo Finnigan RAW file (%s)" % ( data.nice_size( dataset.get_size() ) )


if hasattr(Binary, 'register_sniffable_binary_format'):
    Binary.register_sniffable_binary_format('raw', 'raw', RAW)


class Msp( Text ):
    """ Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf """
    file_ext = "msp"
    
    @staticmethod
    def next_line_starts_with(contents, prefix):

                return False

        return True

# unsniffable binary format, should do something about this
class XHunterAslFormat( Binary ):
    """ Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html """
    file_ext = "hlf"

if hasattr(Binary, 'register_unsniffable_binary_ext'):
    Binary.register_unsniffable_binary_ext('hlf')