Mercurial > repos > completegenomics > cg_cgatools_linux

comparison cgatools/lib/galaxy/datatypes/completegenomics.py @ 0:182426b32995 draft default tip

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author completegenomics
date Mon, 18 Jun 2012 20:15:00 -0400
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1 """
2 Complete Genomics datatypes
3 Birgit Crain - Complete Genomics, Inc
4 """
5
6 import pkg_resources
7 pkg_resources.require( "bx-python" )
8
9 import logging
10 from galaxy.datatypes import data
11 from galaxy import util
12 from cgi import escape
13 from galaxy.datatypes import metadata
14 from galaxy.datatypes import tabular
15 from galaxy.datatypes.metadata import MetadataElement
16 from galaxy.datatypes.tabular import Tabular
17 import galaxy_utils.sequence.vcf
18 from galaxy.datatypes.sniff import *
19
20 log = logging.getLogger(__name__)
21
22 class CG_Var( Tabular ):
23 file_ext = 'cg_var'
24 def __init__(self, **kwd):
25 """Initialize CG_Var datatype"""
26 Tabular.__init__( self, **kwd )
27 self.column_names = ['locus', 'ploidy', 'allele', 'chromosome', 'begin', 'end',
28 'varType', 'reference', 'alleleSeq', 'varScoreVAF',
29 'varScoreEAF', 'varQuality', 'hapLink', 'xRef'
30 ]
31 def display_peek( self, dataset ):
32 """Returns formated html of peek"""
33 return Tabular.make_html_table( self, dataset, column_names=self.column_names )
34
35 class CG_MasterVar( Tabular ):
36 file_ext = 'cg_mastervar'
37 def __init__(self, **kwd):
38 """Initialize CG_MasterVar datatype"""
39 Tabular.__init__( self, **kwd )
40 self.column_names = ['locus', 'ploidy', 'chromosome', 'begin', 'end', 'zygosity',
41 'varType', 'reference', 'allele1Seq', 'allele2Seq',
42 'allele1VarScoreVAF', 'allele2VarScoreVAF', 'allele1VarScoreEAF',
43 'allele2VarScoreEAF', 'allele1VarQuality', 'allele2VarQuality',
44 'allele1HapLink', 'allele2HapLink', 'allele1XRef', 'allele2XRef',
45 'evidenceIntervalId', 'allele1ReadCount', 'allele2ReadCount',
46 'referenceAlleleRead', 'totalReadCount', 'allele1Gene',
47 'allele2Gene pfam', 'miRBaseId', 'repeatMasker', 'segDupOverlap',
48 'relativeCoverageDiploid', 'calledPloidy',
49 'relativeCoverageNondiploid', 'calledLevel'
50 ]
51
52 def display_peek( self, dataset ):
53 """Returns formated html of peek"""
54 return Tabular.make_html_table( self, dataset, column_names=self.column_names )
55
56 class CG_Gene( Tabular ):
57 file_ext = 'cg_gene'
58 def __init__(self, **kwd):
59 """Initialize CG_Gene datatype"""
60 Tabular.__init__( self, **kwd )
61 self.column_names = ['index', 'locus', 'allele', 'chromosome', 'begin', 'end',
62 'varType', 'reference', 'call', 'xRef', 'geneId',
63 'mrnaAcc', 'proteinAcc', 'symbol', 'orientation', 'component',
64 'componentIndex', 'hasCodingRegion', 'impact', 'nucleotidePos',
65 'proteinPos', 'annotationRefSequence', 'sampleSequence',
66 'genomeRefSequence', 'pfam'
67 ]
68
69 def display_peek( self, dataset ):
70 """Returns formated html of peek"""
71 return Tabular.make_html_table( self, dataset, column_names=self.column_names )