Mercurial > repos > jjohnson > snpeff_datatypes
changeset 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 | |
| files | snpeff.py |
| diffstat | 1 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/snpeff.py Tue Jan 13 12:30:20 2015 -0600 +++ b/snpeff.py Wed Jan 14 11:53:36 2015 -0600 @@ -12,7 +12,7 @@ """Class describing a SnpEff genome build""" file_ext = "snpeffdb" MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None ) - MetadataElement( name="snpeff_version", default=None, desc="SnpEff Version", readonly=True, visible=True, no_value=None ) + MetadataElement( name="snpeff_version", default="SnpEff4.0", desc="SnpEff Version", readonly=True, visible=True, no_value=None ) MetadataElement( name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[], optional=True) MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True) @@ -52,6 +52,7 @@ genome_version = os.path.basename(root) dataset.metadata.genome_version = genome_version # read the first line of the gzipped snpEffectPredictor.bin file to get the SnpEff version + # Starting with version 4.1, this should be: SnpEff 4.1 snpeff_version = self.getSnpeffVersionFromFile(os.path.join(root,fname)) if snpeff_version: dataset.metadata.snpeff_version = snpeff_version