diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py index aba84208e76..b8688a79f9e 100644 --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -355,12 +355,28 @@ class SnpEffDb( Text ): """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="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) def __init__( self, **kwd ): Text.__init__( self, **kwd ) + # The SnpEff version line was added in SnpEff version 4.1 + def getSnpeffVersionFromFile(self, path): + snpeff_version = None + try: + fh = gzip.open(path, 'rb') + buf = fh.read(100) + lines = buf.splitlines() + m = re.match('^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip()) + if m: + snpeff_version = m.groups()[0] + m.groups()[1] + fh.close() + except: + pass + return snpeff_version + def set_meta( self, dataset, **kwd ): Text.set_meta(self, dataset, **kwd ) data_dir = dataset.extra_files_path @@ -370,6 +386,8 @@ class SnpEffDb( Text ): annotations_dict = {'nextProt.bin' : '-nextprot', 'motif.bin': '-motif'} regulations = [] annotations = [] + genome_version = None + snpeff_version = None if data_dir and os.path.isdir(data_dir): for root, dirs, files in os.walk(data_dir): for fname in files: @@ -377,6 +395,10 @@ class SnpEffDb( Text ): # if snpEffectPredictor.bin download succeeded 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 + snpeff_version = self.getSnpeffVersionFromFile(os.path.join(root, fname)) + if snpeff_version: + dataset.metadata.snpeff_version = snpeff_version else: m = re.match(regulation_pattern, fname) if m: @@ -390,7 +412,8 @@ class SnpEffDb( Text ): dataset.metadata.annotation = annotations try: fh = file(dataset.file_name, 'w') - fh.write("%s\n" % genome_version) + fh.write("%s\n" % genome_version if genome_version else 'Genome unknown') + fh.write("%s\n" % snpeff_version if snpeff_version else 'SnpEff version unknown') if annotations: fh.write("annotations: %s\n" % ','.join(annotations)) if regulations: @@ -422,8 +445,8 @@ class SnpSiftDbNSFP( Text ): """ def __init__( self, **kwd ): Text.__init__( self, **kwd ) - self.add_composite_file( '%s.grp', description='Group File', substitute_name_with_metadata='reference_name', is_binary=False ) - self.add_composite_file( '%s.ti', description='', substitute_name_with_metadata='reference_name', is_binary=False ) + self.add_composite_file( '%s.gz', description='dbNSFP bgzip', substitute_name_with_metadata='reference_name', is_binary=True ) + self.add_composite_file( '%s.gz.tbi', description='Tabix Index File', substitute_name_with_metadata='reference_name', is_binary=True ) def init_meta( self, dataset, copy_from=None ): Text.init_meta( self, dataset, copy_from=copy_from ) @@ -471,3 +494,11 @@ class SnpSiftDbNSFP( Text ): self.regenerate_primary_file(dataset) except Exception as e: log.warn("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e))) + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = '%s : %s' % (dataset.metadata.reference_name, ','.join(dataset.metadata.annotation)) + dataset.blurb = '%s' % dataset.metadata.reference_name + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disc'