Mercurial > repos > yufei-luo > s_mart
view commons/core/parsing/ElandParser.py @ 14:c79b9ae3f65f
Deleted selected files
author | m-zytnicki |
---|---|
date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
children |
line wrap: on
line source
# # 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.MapperParser import MapperParser from SMART.Java.Python.structure import Mapping class ElandParser(MapperParser): """A class that parses ELAND format""" def __init__(self, fileName, verbosity = 0): super(ElandParser, self).__init__(fileName, verbosity) def __del__(self): super(ElandParser, self).__del__() def getFileFormats(): return ["eland"] getFileFormats = staticmethod(getFileFormats) def skipFirstLines(self): pass def getInfos(self): super(ElandParser, self).getInfos() def parseLine(self, line): line = line.strip() fields = line.split("\t") if len(fields) < 22: sys.exit("Line %d '%s' does not look like a ELAND line (number of fields is %d instead of 22)" % (self.currentLineNb, line, len(fields))) flowCell = fields[0] run = fields[1] lane = fields[2] tile = fields[3] xcoord = fields[4] ycoord = fields[5] index = fields[6] number = fields[7] read = fields[8] quality = fields[9] chromosome = fields[10] contig = fields[11] position = fields[12] strand = fields[13] description = fields[14] singleScore = fields[15] pairScore = fields[16] partnerChromosome = fields[17] partnerContig = fields[18] partnerOffset = fields[19] partnerStrand = fields[20] filtering = fields[21] if number != "1": sys.exit("S-MART cannot handle pair-end reads yet!") # nothing found if position == "": return None name = "%s_%s:%s:%s:%s:%s#0/1" % (flowCell, run, lane, tile, xcoord, ycoord) direction = 1 if strand == "F" else -1 nbMismatches = 0 for char in description: if ord("A") <= ord(char) and ord(char) <= ord("Z"): nbMismatches += 1 mapping = Mapping() mapping.setTagValue("qualityString", quality) mapping.queryInterval.setName(name) mapping.queryInterval.setDirection(direction) mapping.queryInterval.setStart(1) mapping.queryInterval.setEnd(len(read)) mapping.targetInterval.setChromosome(chromosome) mapping.targetInterval.setStart(int(position)) mapping.targetInterval.setEnd(int(position) + len(read)) mapping.targetInterval.setDirection(1) mapping.setSize(len(read)) mapping.setDirection(direction) mapping.setNbGaps(0) mapping.setNbMismatches(nbMismatches) mapping.setTagValue("score", int(singleScore)) if filtering == "Y": return mapping # mapping filtered out return None