annotate commons/core/writer/Gff3Writer.py @ 58:5f5c9b74c2dd

Uploaded
author m-zytnicki
date Fri, 07 Feb 2014 11:53:36 -0500
parents 769e306b7933
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 # Copyright INRA-URGI 2009-2010
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 # This software is governed by the CeCILL license under French law and
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 # abiding by the rules of distribution of free software. You can use,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 # modify and/ or redistribute the software under the terms of the CeCILL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 # license as circulated by CEA, CNRS and INRIA at the following URL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 # "http://www.cecill.info".
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 # As a counterpart to the access to the source code and rights to copy,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 # modify and redistribute granted by the license, users are provided only
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 # with a limited warranty and the software's author, the holder of the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 # economic rights, and the successive licensors have only limited
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 # liability.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 # In this respect, the user's attention is drawn to the risks associated
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 # with loading, using, modifying and/or developing or reproducing the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 # software by the user in light of its specific status of free software,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 # that may mean that it is complicated to manipulate, and that also
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 # therefore means that it is reserved for developers and experienced
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 # professionals having in-depth computer knowledge. Users are therefore
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 # encouraged to load and test the software's suitability as regards their
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 # requirements in conditions enabling the security of their systems and/or
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 # data to be ensured and, more generally, to use and operate it in the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 # same conditions as regards security.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 # The fact that you are presently reading this means that you have had
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 # knowledge of the CeCILL license and that you accept its terms.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 from commons.core.writer.TranscriptListWriter import TranscriptListWriter
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 class Gff3Writer(TranscriptListWriter):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 A class that writes a transcript list into a file with GFF3 format
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 @ivar fileName: name of the file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 @type fileName: string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 @ivar handle: handle to the file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 @type handle: file handle
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 def __init__(self, fileName, verbosity = 0, title="S-MART", feature="transcript", featurePart="exon"):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 Constructor
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 @param fileName: name of the file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 @type fileName: string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 @param verbosity: verbosity
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 @type verbosity: int
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 self.header = ""
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 self.title = title
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 self.feature = feature
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 self.featurePart = featurePart
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 super(Gff3Writer, self).__init__(fileName, verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 @staticmethod
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 def getFileFormats():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 Get the format of the file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 return ["gff3", "gff"]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 @staticmethod
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 def getExtension():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 Get the usual extension for the file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 return "gff3"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 def setTitle(self, title):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 Set the title of the transcripts
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77 @param title: the title of the transcripts
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
78 @type title: string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
79 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
80 self.title = title
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
81
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
82 def setFeature(self, feature):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
83 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
84 Set the name of the feature
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
85 @param title: the title of the feature
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
86 @type feature: string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
87 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
88 self.feature = feature
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
89
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
90 def setFeaturePart(self, featurePart):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
91 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
92 Set the name of the feature part
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
93 @param title: the title of the feature part
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
94 @type featurePart: string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
95 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
96 self.featurePart = featurePart
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
97
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
98
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
99 def printTranscript(self, transcript):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
100 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
101 Export the given transcript with GFF2 format
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
102 @param transcript: transcript to be printed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
103 @type transcript: class L{Transcript<Transcript>}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
104 @return: a string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
105 """
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
106 direction = "+"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
107 if transcript.getDirection() == -1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
108 direction = "-"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
109 transcript.sortExonsIncreasing()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
110 if "ID" not in transcript.getTagValues():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
111 transcript.setTagValue("ID", transcript.getUniqueName())
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
112 feature = self.feature
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
113 tags = transcript.tags
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
114 if "feature" in transcript.getTagNames():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
115 feature = transcript.getTagValue("feature")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
116 del transcript.tags["feature"]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
117 score = "."
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
118 if "score" in transcript.getTagNames():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
119 score = "%d" % (int(transcript.getTagValue("score")))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
120 del transcript.tags["score"]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
121 comment = transcript.getTagValues(";", "=")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
123 if len(transcript.exons) > 1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
124 for i, exon in enumerate(transcript.getExons()):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
125 if "score" in exon.getTagNames():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
126 score = "%d" % (int(exon.getTagValue("score")))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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"))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
128 self.tags = tags
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
129 return string
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
130