Mercurial > repos > yufei-luo > s_mart

comparison commons/core/parsing/ElandParser.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 import sys
31 from commons.core.parsing.MapperParser import MapperParser
32 from SMART.Java.Python.structure import Mapping
33
34 class ElandParser(MapperParser):
35 """A class that parses ELAND format"""
36
37 def __init__(self, fileName, verbosity = 0):
38 super(ElandParser, self).__init__(fileName, verbosity)
39
40
41 def __del__(self):
42 super(ElandParser, self).__del__()
43
44
45 def getFileFormats():
46 return ["eland"]
47 getFileFormats = staticmethod(getFileFormats)
48
49
50 def skipFirstLines(self):
51 pass
52
53
54 def getInfos(self):
55 super(ElandParser, self).getInfos()
56
57
58 def parseLine(self, line):
59
60 line = line.strip()
61
62 fields = line.split("\t")
63 if len(fields) < 22:
64 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)))
65
66 flowCell = fields[0]
67 run = fields[1]
68 lane = fields[2]
69 tile = fields[3]
70 xcoord = fields[4]
71 ycoord = fields[5]
72 index = fields[6]
73 number = fields[7]
74 read = fields[8]
75 quality = fields[9]
76 chromosome = fields[10]
77 contig = fields[11]
78 position = fields[12]
79 strand = fields[13]
80 description = fields[14]
81 singleScore = fields[15]
82 pairScore = fields[16]
83 partnerChromosome = fields[17]
84 partnerContig = fields[18]
85 partnerOffset = fields[19]
86 partnerStrand = fields[20]
87 filtering = fields[21]
88
89 if number != "1":
90 sys.exit("S-MART cannot handle pair-end reads yet!")
91
92 # nothing found
93 if position == "":
94 return None
95
96 name = "%s_%s:%s:%s:%s:%s#0/1" % (flowCell, run, lane, tile, xcoord, ycoord)
97 direction = 1 if strand == "F" else -1
98 nbMismatches = 0
99 for char in description:
100 if ord("A") <= ord(char) and ord(char) <= ord("Z"):
101 nbMismatches += 1
102
103 mapping = Mapping()
104 mapping.setTagValue("qualityString", quality)
105
106 mapping.queryInterval.setName(name)
107 mapping.queryInterval.setDirection(direction)
108 mapping.queryInterval.setStart(1)
109 mapping.queryInterval.setEnd(len(read))
110
111 mapping.targetInterval.setChromosome(chromosome)
112 mapping.targetInterval.setStart(int(position))
113 mapping.targetInterval.setEnd(int(position) + len(read))
114 mapping.targetInterval.setDirection(1)
115
116 mapping.setSize(len(read))
117 mapping.setDirection(direction)
118
119 mapping.setNbGaps(0)
120 mapping.setNbMismatches(nbMismatches)
121 mapping.setTagValue("score", int(singleScore))
122
123 if filtering == "Y":
124 return mapping
125 # mapping filtered out
126 return None