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AlignAce.py

# Copyright 2003 by Bartek Wilczynski.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Parsing AlignACE and CompareACE files: AlignAceParser,CompareAceParser
"""

from Bio.Motif import Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq


00014 class Record:
    def __init__(self):
        self.motifs=[]
        self.current_motif=None
        self.param_dict = None


def read(handle):
    """read(handle)"""
    record = Record()
    record.ver = handle.next()
    record.cmd_line = handle.next()
    for line in handle:
        if line.strip() == "":
            pass
        elif line[:4]=="Para":
            record.param_dict={}
        elif line[0]=="#":
            seq_name = line.split("\t")[1]
            record.seq_dict.append(seq_name)
        elif "=" in line:
            par_name = line.split("=")[0].strip()
            par_value = line.split("=")[1].strip()
            record.param_dict[par_name]=par_value
        elif line[:5]=="Input":
            record.seq_dict=[]
        elif line[:5]=="Motif":
            record.current_motif = Motif()
            record.motifs.append(record.current_motif)
            record.current_motif.alphabet=IUPAC.unambiguous_dna
        elif line[:3]=="MAP":
            record.current_motif.score = float(line.split()[-1])
        elif len(line.split("\t"))==4:
            seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
            record.current_motif.add_instance(seq)
        elif "*" in line:
            record.current_motif.set_mask(line.strip("\n\c"))
        else:
            raise ValueError(line)
    return record


# Everything below is deprecated.

from Bio.ParserSupport import *
import Bio


00062 class AlignAceConsumer:
    """
    The general purpose consumer for the AlignAceScanner (DEPRECATED).

    Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.

    This class is DEPRECATED; please use the read() function in this module
    instead.
    """
    def __init__(self):
        import warnings
        warnings.warn("Bio.Motif.Parsers.AlignAce.AlignAceConsumer is deprecated; please use the read() function in this module instead.", Bio.BiopythonDeprecationWarning)
        self.motifs=[]
        self.current_motif=None
        self.param_dict = None
    
    def parameters(self,line):
        self.param_dict={}

    def parameter(self,line):
        par_name = line.split("=")[0].strip()
        par_value = line.split("=")[1].strip()
        self.param_dict[par_name]=par_value
        
    def sequences(self,line):
        self.seq_dict=[]
        
    def sequence(self,line):
        seq_name = line.split("\t")[1]
        self.seq_dict.append(seq_name)
        
    def motif(self,line):
        self.current_motif = Motif()
        self.motifs.append(self.current_motif)
        self.current_motif.alphabet=IUPAC.unambiguous_dna
        
    def motif_hit(self,line):
        seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
        self.current_motif.add_instance(seq)
        
    def motif_score(self,line):
        self.current_motif.score = float(line.split()[-1])
        
    def motif_mask(self,line):
        self.current_motif.set_mask(line.strip("\n\c"))

    def noevent(self,line):
        pass
        
    def version(self,line):
        self.ver = line
        
    def command_line(self,line):
        self.cmd_line = line
    
00117 class AlignAceParser(AbstractParser):
    """Parses AlignAce data into a sequence of Motifs (DEPRECATED)

    This class is DEPRECATED; please use the read() function in this module
    instead.
    """
00123     def __init__(self):
        """__init__(self)"""
        import warnings
        warnings.warn("Bio.Motif.Parsers.AlignAce.AlignAceParser is deprecated; please use the read() function in this module instead.", Bio.BiopythonDeprecationWarning)
        self._scanner = AlignAceScanner()
        self._consumer = AlignAceConsumer()

00130     def parse(self, handle):
        """parse(self, handle)"""
        self._scanner.feed(handle, self._consumer)
        return self._consumer

00135 class AlignAceScanner:
    """Scannner for AlignACE output (DEPRECATED).

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    noevent - blank line

    version - AlignACE version number
    command_line - AlignACE command line string
    parameters - the begining of the parameters
    parameter - the line containing a parameter
    sequences - the begining of the sequences list
    sequence - line containing the name of the input sequence (and a respective number)
    motif - the begining of the motif (contains the number)
    motif_hit - one hit for a motif
    motif_mask - mask of the motif (space - gap, asterisk - significant position)
    motif_score - MAP score of the motif - approx. N * log R, where R == (num. of actual occur.) / (num. of occur. expected by random.)
    
    This class is DEPRECATED; please use the read() function in this module
    instead.
    """
    def __init__(self):
        import warnings
        warnings.warn("Bio.Motif.Parsers.AlignAce.AlignAceScanner is deprecated; please use the read() function in this module instead.", Bio.BiopythonDeprecationWarning)

00163     def feed(self, handle, consumer):
        """S.feed(handle, consumer)

        Feed in a AlignACE report for scanning.  handle is a file-like
        object that contains the AlignACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """
        consumer.version(handle.readline())
        consumer.command_line(handle.readline())
        for line in handle:
            if line.strip() == "":
                consumer.noevent(line)
            elif line[:4]=="Para":
                consumer.parameters(line)
            elif line[0]=="#":
                consumer.sequence(line)
            elif "=" in line:
                consumer.parameter(line)
            elif line[:5]=="Input":
                consumer.sequences(line)
            elif line[:5]=="Motif":
                consumer.motif(line)
            elif line[:3]=="MAP":
                consumer.motif_score(line)
            elif len(line.split("\t"))==4:
                consumer.motif_hit(line)
            elif "*" in line:
                consumer.motif_mask(line)
            else:
                raise ValueError(line)

00194 class CompareAceScanner:
    """Scannner for CompareACE output (DEPRECATED).

    Methods:
    feed     Feed data into the scanner.

    The scanner generates (and calls the consumer) the following types of events:

    motif_score - CompareACE score of motifs

    ###### TO DO #############3
    extend the scanner to include other, more complex outputs.
    """
    def __init__(self):
        import warnings
        warnings.warn("Bio.Motif.Parsers.AlignAce.CompareAceScanner is deprecated.", Bio.BiopythonDeprecationWarning)

00211     def feed(self, handle, consumer):
        """S.feed(handle, consumer)

        Feed in a CompareACE report for scanning.  handle is a file-like
        object that contains the CompareACE report.  consumer is a Consumer
        object that will receive events as the report is scanned.
        """
        consumer.motif_score(handle.readline())


00221 class CompareAceConsumer:
    """
    The general purpose consumer for the CompareAceScanner (DEPRECATED).

    Should be passed as the consumer to the feed method of the CompareAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
    """
    def __init__(self):
        import warnings
        warnings.warn("Bio.Motif.Parsers.AlignAce.CompareAceConsumer is deprecated.", Bio.BiopythonDeprecationWarning)

    def motif_score(self,line):
        self.data = float(line.split()[-1])
    
00234 class CompareAceParser(AbstractParser):
    """Parses CompareAce output to usable form

    ### so far only in a very limited way
    """
00239     def __init__(self):
        """__init__(self)"""
        import warnings
        warnings.warn("CompareAceParser and ComparAceConsumer are" \
              +" deprecated, and will be removed in a future release of"\
              +" Biopython. If you want to continue to use this code,"\
              +" please get in contact with the Biopython developers via"\
              +" the mailing lists to avoid its permanent removal from"\
              +" Biopython. See also the Python built in set datatype.", \
              Bio.BiopythonDeprecationWarning)
        self._scanner = CompareAceScanner()
        self._consumer = CompareAceConsumer()

00252     def parse(self, handle):
        """parse(self, handle)"""
        self._scanner.feed(handle, self._consumer)
        return self._consumer.data

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