|
0
|
1 """
|
|
|
2 SnpSift dbNSFP datatypes
|
|
|
3 """
|
|
|
4 import os,os.path,re,sys,gzip,logging
|
|
|
5 import traceback
|
|
|
6 import galaxy.datatypes.data
|
|
|
7 from galaxy.datatypes.data import Text
|
|
|
8 from galaxy.datatypes.metadata import MetadataElement
|
|
|
9
|
|
|
10 log = logging.getLogger(__name__)
|
|
|
11
|
|
|
12 class SnpSiftDbNSFP( Text ):
|
|
|
13 """Class describing a dbNSFP database prepared fpr use by SnpSift dbnsfp """
|
|
|
14 MetadataElement( name='reference_name', default='dbSNFP' , desc='Reference Name', readonly=True, visible=True, set_in_upload=True, no_value='dbSNFP' )
|
|
|
15 MetadataElement( name="bgzip", default=None, desc="dbNSFP bgzip", readonly=True, visible=True, no_value=None )
|
|
|
16 MetadataElement( name="index", default=None, desc="Tabix Index File", readonly=True, visible=True, no_value=None)
|
|
|
17 MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[] )
|
|
|
18 file_ext = "snpsiftdbnsfp"
|
|
|
19 composite_type = 'auto_primary_file'
|
|
|
20 allow_datatype_change = False
|
|
|
21 """
|
|
|
22 ## The dbNSFP file is a tabular file with 1 header line
|
|
|
23 ## The first 4 columns are required to be: chrom pos ref alt
|
|
|
24 ## These match columns 1,2,4,5 of the VCF file
|
|
|
25 ## SnpSift requires the file to be block-gzipped and the indexed with samtools tabix
|
|
|
26 ## Example:
|
|
|
27 ## Compress using block-gzip algorithm
|
|
|
28 bgzip dbNSFP2.3.txt
|
|
|
29 ## Create tabix index
|
|
|
30 tabix -s 1 -b 2 -e 2 dbNSFP2.3.txt.gz
|
|
|
31 """
|
|
|
32 def __init__( self, **kwd ):
|
|
|
33 Text.__init__( self, **kwd )
|
|
|
34 self.add_composite_file( '%s.grp', description = 'Group File', substitute_name_with_metadata = 'reference_name', is_binary = False )
|
|
|
35 self.add_composite_file( '%s.ti', description = '', substitute_name_with_metadata = 'reference_name', is_binary = False )
|
|
|
36 def init_meta( self, dataset, copy_from=None ):
|
|
|
37 Text.init_meta( self, dataset, copy_from=copy_from )
|
|
|
38 def generate_primary_file( self, dataset = None ):
|
|
|
39 """
|
|
|
40 This is called only at upload to write the html file
|
|
|
41 cannot rename the datasets here - they come with the default unfortunately
|
|
|
42 """
|
|
|
43 regenerate_primary_file( self, dataset)
|
|
|
44 def regenerate_primary_file(self,dataset):
|
|
|
45 """
|
|
|
46 cannot do this until we are setting metadata
|
|
|
47 """
|
|
|
48 annotations = "dbNSFP Annotations: %s\n" % ','.join(dataset.metadata.annotation)
|
|
|
49 f = open(dataset.file_name,'a')
|
|
|
50 if dataset.metadata.bgzip:
|
|
|
51 bn = dataset.metadata.bgzip
|
|
|
52 f.write(bn)
|
|
|
53 f.write('\n')
|
|
|
54 f.write(annotations)
|
|
|
55 f.close()
|
|
|
56 def set_meta( self, dataset, overwrite=True, **kwd ):
|
|
|
57 try:
|
|
|
58 efp = dataset.extra_files_path
|
|
|
59 if os.path.exists(efp):
|
|
|
60 flist = os.listdir(efp)
|
|
|
61 for i,fname in enumerate(flist):
|
|
|
62 if fname.endswith('.gz'):
|
|
|
63 dataset.metadata.bgzip = fname
|
|
|
64 try:
|
|
|
65 fh = gzip.open(os.path.join(efp,fname),'r')
|
|
|
66 buf = fh.read(5000)
|
|
|
67 lines = buf.splitlines()
|
|
|
68 headers = lines[0].split('\t')
|
|
|
69 dataset.metadata.annotation = headers[4:]
|
|
|
70 except Exception,e:
|
|
|
71 log.warn("set_meta fname: %s %s" % (fname,str(e)))
|
|
|
72 traceback.print_stack(file=sys.stderr)
|
|
|
73 finally:
|
|
|
74 fh.close()
|
|
|
75 if fname.endswith('.tbi'):
|
|
|
76 dataset.metadata.index = fname
|
|
|
77 self.regenerate_primary_file(dataset)
|
|
|
78 except Exception,e:
|
|
|
79 log.warn("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown',str(e)))
|
|
|
80 traceback.print_stack(file=sys.stderr)
|
|
|
81
|
|
|
82 if __name__ == '__main__':
|
|
|
83 import doctest
|
|
|
84 doctest.testmod(sys.modules[__name__])
|
|
|
85
|
