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Merge pull request #1280 from jj-umn/patch-2

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Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1
This commit is contained in:
John Chilton
2016-02-12 16:23:28 -05:00
parent 063c5ad0f8 acef6ab3f9
commit 8fb3e461ac
1 changed files with 34 additions and 3 deletions
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lib/galaxy/datatypes/text.py
+34 -3
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@@ -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'