Mercurial > repos > yufei-luo > s_mart

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

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 94ab73e8a190
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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.SequenceListParser import SequenceListParser
32 from SMART.Java.Python.structure.Sequence import Sequence
33 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
34
35 class FastaParser(SequenceListParser):
36 """A class that reads a list of sequences in FASTA"""
37
38 def __init__(self, fileName, verbosity = 0):
39 super(FastaParser, self).__init__(fileName, verbosity)
40 self.tags = {}
41
42
43 def getTags(self):
44 return self.tags
45
46
47 def getFileFormats():
48 return ["fasta", "mfa", "fas"]
49 getFileFormats = staticmethod(getFileFormats)
50
51
52 def getInfos(self):
53 """
54 Get some generic information about the sequences
55 """
56 self.nbSequences = 0
57 self.size = 0
58 self.reset()
59 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity - 9)
60 for line in self.handle:
61 line = line.strip()
62 if line == "":
63 continue
64 if line[0] == ">":
65 self.nbSequences += 1
66 else:
67 self.size += len(line)
68 progress.inc()
69 progress.done()
70 self.reset()
71
72
73 def parseOne(self):
74 """
75 Parse only one element in the file
76 """
77 name = None
78 string = ""
79
80 if self.currentLine != None:
81 if self.currentLine[0] != ">":
82 raise Exception("First line is weird: %s" % (self.currentLine))
83 name = self.currentLine[1:].split()[0]
84 self.currentLine = None
85
86 for line in self.handle:
87 line = line.strip()
88 if line == "":
89 pass
90 elif line[0] == ">":
91 if name == None:
92 name = line[1:].split()[0]
93 else:
94 self.currentLine = line
95 return Sequence(name, string)
96 else:
97 string += line
98
99 if name == None:
100 return None
101 return Sequence(name, string)
102
103
104 def setTags(self):
105 mark = self.handle.tell()
106 thisTag = mark
107
108 line = self.handle.readline()
109 while line != "":
110 if line[0] == ">":
111 line = line.strip()
112 self.tags[line[1:].split()[0]] = thisTag
113 thisTag = self.handle.tell()
114 line = self.handle.readline()
115
116 self.handle.seek(mark)
117
118
119 def getSubSequence(self, chromosome, start, end, direction, name = None):
120 if not self.tags:
121 self.setTags()
122
123 if chromosome not in self.tags:
124 raise Exception("Cannot find " + chromosome)
125
126 if name == None:
127 name = "%s:%d-%d (%d)" % (chromosome, start, end, direction)
128 sequence = Sequence(name)
129
130 # switch from 0-based to 1-based coordinates
131 start -= 1
132 end -= 1
133
134 self.handle.seek(self.tags[chromosome])
135 line = self.handle.readline().strip()
136 if line != ">" + chromosome:
137 raise Exception("Arrived in a wrong place (got %s)" % (line))
138
139 position1 = self.handle.tell()
140 line = self.handle.readline().strip()
141 position2 = self.handle.tell()
142 size = len(line)
143 address = position1 + ((start - (start % size)) / size) * (position2 - position1);
144
145 count = max(0, start - (start % size));
146 self.handle.seek(address)
147
148 newSequence = ""
149 for line in self.handle:
150 line = line.strip()
151
152 if line[0] == ">":
153 break
154
155 subStart = start - count
156 if subStart < 0:
157 subStart = 0
158 subEnd = end - count
159 subSize = subEnd - subStart + 1
160 if subSize + subStart > len(line):
161 subSize = len(line) - subStart
162 if subEnd < 0:
163 break
164 if subStart <= len(line):
165 newSequence += line[subStart:subStart+subSize]
166 count += len(line)
167
168 if newSequence == "":
169 raise Exception("Error, sequence %s is empty" % (name))
170 sequence.sequence = newSequence
171 if direction == -1:
172 sequence.reverseComplement()
173 return sequence