Mercurial > repos > jjohnson > snpeff_datatypes
comparison snpeff.py @ 4:5d6f3622b99d default tip
Default to snpeff_version: SnpEff4.0
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 14 Jan 2015 11:53:36 -0600 |
| parents | 9efd0d32fe8a |
| children |
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| 3:9efd0d32fe8a | 4:5d6f3622b99d |
|---|---|
| 10 | 10 |
| 11 class SnpEffDb( Text ): | 11 class SnpEffDb( Text ): |
| 12 """Class describing a SnpEff genome build""" | 12 """Class describing a SnpEff genome build""" |
| 13 file_ext = "snpeffdb" | 13 file_ext = "snpeffdb" |
| 14 MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None ) | 14 MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None ) |
| 15 MetadataElement( name="snpeff_version", default=None, desc="SnpEff 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) | 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) | 17 MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True) |
| 18 | 18 |
| 19 def __init__( self, **kwd ): | 19 def __init__( self, **kwd ): |
| 20 Text.__init__( self, **kwd ) | 20 Text.__init__( self, **kwd ) |
| 50 if fname.startswith('snpEffectPredictor'): | 50 if fname.startswith('snpEffectPredictor'): |
| 51 # if snpEffectPredictor.bin download succeeded | 51 # if snpEffectPredictor.bin download succeeded |
| 52 genome_version = os.path.basename(root) | 52 genome_version = os.path.basename(root) |
| 53 dataset.metadata.genome_version = genome_version | 53 dataset.metadata.genome_version = genome_version |
| 54 # read the first line of the gzipped snpEffectPredictor.bin file to get the SnpEff version | 54 # read the first line of the gzipped snpEffectPredictor.bin file to get the SnpEff version |
| 55 # Starting with version 4.1, this should be: SnpEff 4.1 | |
| 55 snpeff_version = self.getSnpeffVersionFromFile(os.path.join(root,fname)) | 56 snpeff_version = self.getSnpeffVersionFromFile(os.path.join(root,fname)) |
| 56 if snpeff_version: | 57 if snpeff_version: |
| 57 dataset.metadata.snpeff_version = snpeff_version | 58 dataset.metadata.snpeff_version = snpeff_version |
| 58 else: | 59 else: |
| 59 m = re.match(regulation_pattern,fname) | 60 m = re.match(regulation_pattern,fname) |