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