Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/Gff3Writer.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 from commons.core.writer.TranscriptListWriter import TranscriptListWriter
31
32
33 class Gff3Writer(TranscriptListWriter):
34 """
35 A class that writes a transcript list into a file with GFF3 format
36 @ivar fileName: name of the file
37 @type fileName: string
38 @ivar handle: handle to the file
39 @type handle: file handle
40 """
41
42
43 def __init__(self, fileName, verbosity = 0, title="S-MART", feature="transcript", featurePart="exon"):
44 """
45 Constructor
46 @param fileName: name of the file
47 @type fileName: string
48 @param verbosity: verbosity
49 @type verbosity: int
50 """
51 self.header = ""
52 self.title = title
53 self.feature = feature
54 self.featurePart = featurePart
55 super(Gff3Writer, self).__init__(fileName, verbosity)
56
57
58 @staticmethod
59 def getFileFormats():
60 """
61 Get the format of the file
62 """
63 return ["gff3", "gff"]
64
65
66 @staticmethod
67 def getExtension():
68 """
69 Get the usual extension for the file
70 """
71 return "gff3"
72
73
74 def setTitle(self, title):
75 """
76 Set the title of the transcripts
77 @param title: the title of the transcripts
78 @type title: string
79 """
80 self.title = title
81
82 def setFeature(self, feature):
83 """
84 Set the name of the feature
85 @param title: the title of the feature
86 @type feature: string
87 """
88 self.feature = feature
89
90 def setFeaturePart(self, featurePart):
91 """
92 Set the name of the feature part
93 @param title: the title of the feature part
94 @type featurePart: string
95 """
96 self.featurePart = featurePart
97
98
99 def printTranscript(self, transcript):
100 """
101 Export the given transcript with GFF2 format
102 @param transcript: transcript to be printed
103 @type transcript: class L{Transcript<Transcript>}
104 @return: a string
105 """
106 direction = "+"
107 if transcript.getDirection() == -1:
108 direction = "-"
109 transcript.sortExonsIncreasing()
110 if "ID" not in transcript.getTagValues():
111 transcript.setTagValue("ID", transcript.getUniqueName())
112 feature = self.feature
113 tags = transcript.tags
114 if "feature" in transcript.getTagNames():
115 feature = transcript.getTagValue("feature")
116 del transcript.tags["feature"]
117 score = "."
118 if "score" in transcript.getTagNames():
119 score = "%d" % (int(transcript.getTagValue("score")))
120 del transcript.tags["score"]
121 comment = transcript.getTagValues(";", "=")
122 string = "%s\t%s\t%s\t%d\t%d\t%s\t%s\t.\t%s\n" % (transcript.getChromosome(), self.title, feature, transcript.getStart(), transcript.getEnd(), score, direction, comment)
123 if len(transcript.exons) > 1:
124 for i, exon in enumerate(transcript.getExons()):
125 if "score" in exon.getTagNames():
126 score = "%d" % (int(exon.getTagValue("score")))
127 string += "%s\t%s\t%s\t%d\t%d\t%s\t%s\t.\tID=%s-%s%d;Name=%s-%s%d;Parent=%s\n" % (transcript.getChromosome(), self.title,self.featurePart, exon.getStart(), exon.getEnd(), score, direction, transcript.getTagValue("ID"),self.featurePart, i+1, transcript.name,self.featurePart, i+1, transcript.getTagValue("ID"))
128 self.tags = tags
129 return string
130