Mercurial > repos > iuc > snpeff_datatypes

comparison snpeff.py @ 0:d78b2b2a3388 draft

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author iuc
date Thu, 22 Jan 2015 07:58:16 -0500
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children 2b53f59de80c
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-1:000000000000 0:d78b2b2a3388
1 """
2 SnpEff datatypes
3 """
4 import os,os.path,re,sys,gzip,logging
5 import galaxy.datatypes.data
6 from galaxy.datatypes.data import Text
7 from galaxy.datatypes.metadata import MetadataElement
8
9 log = logging.getLogger(__name__)
10
11 class SnpEffDb( Text ):
12 """Class describing a SnpEff genome build"""
13 file_ext = "snpeffdb"
14 MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None )
15 MetadataElement( name="snpeff_version", default="SnpEff4.0", desc="SnpEff Version", readonly=True, visible=True, no_value=None )
16 MetadataElement( name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[], optional=True)
17 MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True)
18
19 def __init__( self, **kwd ):
20 Text.__init__( self, **kwd )
21
22 "" The SnpEff version line was added in SnpEff version 4.1
23 def getSnpeffVersionFromFile(self, path):
24 snpeff_version = None
25 try:
26 fh = gzip.open(path, 'rb')
27 buf = fh.read(100)
28 lines = buf.splitlines()
29 m = re.match('^(SnpEff)\s+(\d+\.\d+).*$',lines[0].strip())
30 if m:
31 snpeff_version = m.groups()[0] + m.groups()[1]
32 fh.close()
33 except Exception, e:
34 pass
35 return snpeff_version
36
37 def set_meta( self, dataset, **kwd ):
38 Text.set_meta(self, dataset, **kwd )
39 data_dir = dataset.extra_files_path
40 ## search data_dir/genome_version for files
41 regulation_pattern = 'regulation_(.+).bin'
42 # annotation files that are included in snpEff by a flag
43 annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
44 regulations = []
45 annotations = []
46 genome_version = None
47 snpeff_version = None
48 if data_dir and os.path.isdir(data_dir):
49 for root, dirs, files in os.walk(data_dir):
50 for fname in files:
51 if fname.startswith('snpEffectPredictor'):
52 # if snpEffectPredictor.bin download succeeded
53 genome_version = os.path.basename(root)
54 dataset.metadata.genome_version = genome_version
55 else:
56 m = re.match(regulation_pattern,fname)
57 if m:
58 name = m.groups()[0]
59 regulations.append(name)
60 elif fname in annotations_dict:
61 value = annotations_dict[fname]
62 name = value.lstrip('-')
63 annotations.append(name)
64 dataset.metadata.regulation = regulations
65 dataset.metadata.annotation = annotations
66 try:
67 fh = file(dataset.file_name,'w')
68 fh.write("%s\n" % genome_version if genome_version else 'Genome unknown')
69 fh.write("%s\n" % snpeff_version if snpeff_version else 'SnpEff version unknown')
70 if annotations:
71 fh.write("annotations: %s\n" % ','.join(annotations))
72 if regulations:
73 fh.write("regulations: %s\n" % ','.join(regulations))
74 fh.close()
75 except:
76 pass
77