Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/SequenceListParser.py @ 53:47310c4fb725
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author | m-zytnicki |
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date | Fri, 10 Jan 2014 08:57:02 -0500 |
parents | 769e306b7933 |
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# # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # import sys from SMART.Java.Python.structure.SequenceList import SequenceList from SMART.Java.Python.misc.Progress import Progress class SequenceListParser(object): """ A virtual class that reads a list of sequences @ivar verbosity: verbosity @type verbosity: int @ivar fileName: name of the file to parse @type fileName: string @ivar handle: file to parse @type handle: file @ivar nbSequences: number of sequences in the file @type nbSequences: int @ivar nbReadSequences: number of sequences read @type nbReadSequences: int @ivar currentLine: line currently read @type currentLine: string @ivar size: total number of nucleotides in the sequences @type size: int @ivar sizes: number of nucleotides per sequences @type sizes: dict of string to int """ def __init__(self, fileName, verbosity = 0): """ Constructor @param verbosity: verbosity @type verbosity: int @param fileName: name of the file to parse @type fileName: string """ self.verbosity = verbosity self.fileName = fileName self.nbSequences = None self.nbReadSequences = 0 self.currentLine = None self.size = None self.sizes = None try: self.handle = open(self.fileName, "rb") except IOError: raise Exception("Error! Sequence file '%s' does not exist! Exiting..." % (self.fileName)) def __del__(self): """ Destructor """ if not self.handle.closed: self.handle.close() def close(self): """ Close file handle """ self.handle.close() def reset(self): """ Prepare the file to be read again from start """ self.handle.seek(0) self.currentLine = None self.nbReadSequences = 0 def getFileFormats(self): pass getFileFormats = staticmethod(getFileFormats) def parse(self): """ Parse the whole file in one shot @return: a list of sequence """ sequenceList = SequenceList() progress = Progress(self.getNbSequences(), "Reading %s" % (self.fileName), self.verbosity) for sequence in self.getIterator(): sequenceList.addSequence(sequence) progress.inc() progress.done() return sequenceList def getIterator(self): """ Iterate on the file, sequence by sequence @return: an iterator to sequences """ self.reset() sequence = self.parseOne() while sequence != None: self.nbReadSequences += 1 yield sequence sequence = self.parseOne() def getInfos(self): """ Get some generic information about the sequences """ self.nbSequences = 0 self.size = 0 self.reset() if self.verbosity >= 10: print "Getting information on %s." % (self.fileName) for sequence in self.getIterator(): self.nbSequences += 1 self.size += sequence.getSize() if self.verbosity >= 10 and self.nbSequences % 100000 == 0: sys.stdout.write(" %d sequences read\r" % (self.nbSequences)) sys.stdout.flush() self.reset() if self.verbosity >= 10: print " %d sequences read" % (self.nbSequences) print "Done." def getNbSequences(self): """ Get the number of sequences in the file @return: the number of sequences """ if self.nbSequences != None: return self.nbSequences self.getInfos() return self.nbSequences def getNbItems(self): """ Get the number of sequences in the file @return: the number of sequences """ return self.getNbSequences() def getSize(self): """ Get the size of all the sequences @return: the size """ if self.size != None: return self.size self.getInfos() return self.size def getRegions(self): """ Get the names of the sequences @return: the names """ if self.sizes != None: return self.sizes.keys() self.sizes = {} self.reset() if self.verbosity >= 10: print "Getting information on %s." % (self.fileName) self.nbSequences = 0 for sequence in self.getIterator(): self.sizes[sequence.name] = sequence.getSize() self.nbSequences += 1 if self.verbosity >= 10 and self.nbSequences % 100000 == 0: sys.stdout.write(" %d sequences read\r" % (self.nbSequences)) sys.stdout.flush() self.reset() if self.verbosity >= 10: print " %d sequences read" % (self.nbSequences) print "Done." return self.sizes.keys() def getSizeOfRegion(self, region): """ Get the size of a sequence @param region: the name of the sequence @type region: string @return: the size of the sequence """ if self.sizes != None: if region not in self.sizes: raise Exception("Region %s is not found" % region) return self.sizes[region] self.getRegions() if region not in self.sizes: raise Exception("Region %s is not found" % region) def __eq__(self, o): if o == None: return False return self.fileName == o.fileName and self.nbSequences == o.nbSequences