Mercurial > repos > yufei-luo > s_mart
diff commons/core/parsing/ElandParser.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/commons/core/parsing/ElandParser.py Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,126 @@ +# +# 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