annotate commons/core/parsing/FastqParser.py @ 56:97aa2e42bfdf

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#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
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import sys
from commons.core.parsing.SequenceListParser import SequenceListParser
from SMART.Java.Python.structure.Sequence import Sequence

class FastqParser(SequenceListParser):
    """A class that reads a list of sequences in FASTQ format"""

    def __init__(self, fileName, verbosity = 0):
        super(FastqParser, self).__init__(fileName, verbosity)


    def getFileFormats():
        return ["fastq", "mfq"]
    getFileFormats = staticmethod(getFileFormats)


    def getInfos(self):
        """
        Get some generic information about the sequences
        """
        self.nbSequences = 0
        self.reset()
        if self.verbosity >= 10:
            print "Getting information on %s." % (self.fileName)

        nbLines = 0
        for line in self.handle:
            line = line.strip()
            if line == "":
                continue
            nbLines += 1
            if self.verbosity >= 10 and nbLines % 400000 == 0:
                sys.stdout.write("    %d sequences read\r" % (nbLines / 4))
                sys.stdout.flush()
        self.reset()
        self.nbSequences = nbLines / 4
        if self.verbosity >= 10:
            print "    %d sequences read" % (self.nbSequences)
            print "Done."


    def parseOne(self):
        """
        Parse only one element in the file
        """
        string = ""
        quality = ""
        lineType = 0

        for line in self.handle:
            line = line.strip()
            if lineType == 0:
                if line[0] != "@":
                    raise Exception("Line '%s' should start with '@'!" % (line))
                name = line[1:]
                inSequence = True
                inQuality = False
            elif lineType == 1:
                string = line
            elif lineType == 2:
                if line[0] != "+":
                    sys.exit("Line '%s' should start with '+'!" % (line))
                if line[1:] != name and line != "+":
                    sys.exit("Weird difference in sequence and quality names (%s and %s) while parsing FASTQ file %s." % (name, line[1:], self.fileName))
                inQuality = True
                inSequence = False
            elif lineType == 3:
                quality = line
            lineType += 1
            if lineType == 4:
                sequence = Sequence(name, string)
                sequence.setQuality(quality)
                return sequence
                
        return None