Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/FastaParser.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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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 commons.core.parsing.SequenceListParser import SequenceListParser from SMART.Java.Python.structure.Sequence import Sequence from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress class FastaParser(SequenceListParser): """A class that reads a list of sequences in FASTA""" def __init__(self, fileName, verbosity = 0): super(FastaParser, self).__init__(fileName, verbosity) self.tags = {} def getTags(self): return self.tags def getFileFormats(): return ["fasta", "mfa", "fas"] getFileFormats = staticmethod(getFileFormats) def getInfos(self): """ Get some generic information about the sequences """ self.nbSequences = 0 self.size = 0 self.reset() progress = UnlimitedProgress(100000, "Reading input file", self.verbosity - 9) for line in self.handle: line = line.strip() if line == "": continue if line[0] == ">": self.nbSequences += 1 else: self.size += len(line) progress.inc() progress.done() self.reset() def parseOne(self): """ Parse only one element in the file """ name = None string = "" if self.currentLine != None: if self.currentLine[0] != ">": raise Exception("First line is weird: %s" % (self.currentLine)) name = self.currentLine[1:].split()[0] self.currentLine = None for line in self.handle: line = line.strip() if line == "": pass elif line[0] == ">": if name == None: name = line[1:].split()[0] else: self.currentLine = line return Sequence(name, string) else: string += line if name == None: return None return Sequence(name, string) def setTags(self): mark = self.handle.tell() thisTag = mark line = self.handle.readline() while line != "": if line[0] == ">": line = line.strip() self.tags[line[1:].split()[0]] = thisTag thisTag = self.handle.tell() line = self.handle.readline() self.handle.seek(mark) def getSubSequence(self, chromosome, start, end, direction, name = None): if not self.tags: self.setTags() if chromosome not in self.tags: raise Exception("Cannot find " + chromosome) if name == None: name = "%s:%d-%d (%d)" % (chromosome, start, end, direction) sequence = Sequence(name) # switch from 0-based to 1-based coordinates start -= 1 end -= 1 self.handle.seek(self.tags[chromosome]) line = self.handle.readline().strip() if line != ">" + chromosome: raise Exception("Arrived in a wrong place (got %s)" % (line)) position1 = self.handle.tell() line = self.handle.readline().strip() position2 = self.handle.tell() size = len(line) address = position1 + ((start - (start % size)) / size) * (position2 - position1); count = max(0, start - (start % size)); self.handle.seek(address) newSequence = "" for line in self.handle: line = line.strip() if line[0] == ">": break subStart = start - count if subStart < 0: subStart = 0 subEnd = end - count subSize = subEnd - subStart + 1 if subSize + subStart > len(line): subSize = len(line) - subStart if subEnd < 0: break if subStart <= len(line): newSequence += line[subStart:subStart+subSize] count += len(line) if newSequence == "": raise Exception("Error, sequence %s is empty" % (name)) sequence.sequence = newSequence if direction == -1: sequence.reverseComplement() return sequence