Mercurial > repos > iuc > snpeff
diff lib/galaxy/datatypes/snpeff.py @ 0:e8adfc4c0a6b draft
Uploaded
author | iuc |
---|---|
date | Wed, 11 Dec 2013 08:53:32 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/snpeff.py Wed Dec 11 08:53:32 2013 -0500 @@ -0,0 +1,46 @@ +""" +SnpEff datatypes +""" +import os,os.path,re,sys +import galaxy.datatypes.data +from galaxy.datatypes.data import Text +from galaxy.datatypes.metadata import MetadataElement + +class SnpEffDb( Text ): + """Class describing an IGV tiled data file (TDF) .tdf binary file""" + file_ext = "snpeffdb" + MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None ) + MetadataElement( name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[] ) + MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[] ) + + def __init__( self, **kwd ): + Text.__init__( self, **kwd ) + + def set_meta( self, dataset, **kwd ): + Text.set_meta(self, dataset, **kwd ) + data_dir = dataset.extra_files_path + ## search data_dir/genome_version for files + regulation_pattern = 'regulation_(.+).bin' + # annotation files that are included in snpEff by a flag + annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'} + regulations = [] + annotations = [] + if data_dir and os.path.isdir(data_dir): + for root, dirs, files in os.walk(data_dir): + for fname in files: + if fname.startswith('snpEffectPredictor'): + # if snpEffectPredictor.bin download succeeded + genome_version = os.path.basename(root) + dataset.metadata.genome_version = genome_version + else: + m = re.match(regulation_pattern,fname) + if m: + name = m.groups()[0] + regulations.append(name) + elif fname in annotations_dict: + value = annotations_dict[fname] + name = value.lstrip('-') + annotations.append(name) + dataset.metadata.regulation = regulations + dataset.metadata.annotation = annotations +