def run(self):
genome = self.genome
if os.path.isdir(genome):
genome = os.path.join(genome, os.path.split(genome)[1]+'.genome')
print genome
#pref_filename = os.path.join(os.path.expanduser('~'),'igv','prefs.properties')
#if os.path.exists(pref_filename):
# with open(pref_filename,'rb') as f:
# lines = f.readlines()
# with open(pref_filename,'wb') as f:
# for line in lines:
# if line.startswith('DEFAULT_GENOME_KEY='):
# #line = 'DEFAULT_GENOME_KEY=\n'
# continue
# f.write(line)
with workspace.tempspace() as temp:
with open(temp/'batch.txt','wb') as f:
print >> f, 'new'
print >> f, 'preference LAST_TRACK_DIRECTORY', os.getcwd()
print >> f, 'preference LAST_GENOME_IMPORT_DIRECTORY', os.getcwd()
print >> f, 'genome '+os.path.abspath(genome)
for filename in self.files:
print >> f, 'load '+os.path.abspath(filename)
io.execute(['java','-Xmx32000m',
#Flags from igb.sh script:
'-Dproduction=true','-Dapple.laf.useScreenMenuBar=true','-Djava.net.preferIPv4Stack=true',
'-jar',io.find_jar('igv.jar'),'-b',temp/'batch.txt'])
def build_snpeff(self):
jar = io.find_jar('snpEff.jar')
with open(self/'snpeff.config','wb') as f:
print >> f, 'data_dir = snpeff'
print >> f, 'genomes : ' + self.name
print >> f, self.name + '.genome : ' + self.name
snpwork = io.Workspace(self/'snpeff',must_exist=False)
snpwork_genome = io.Workspace(snpwork/self.name,must_exist=False)
snpwork_genomes = io.Workspace(snpwork/'genomes',must_exist=False)
annotations = self.annotations_filename()
assert annotations
with open(snpwork_genome/'genes.gff','wb') as f:
for record in annotation.read_annotations(annotations):
if record.end <= record.start: continue
if not record.attr:
record.attr['attributes'] = 'none'
print >> f, record.as_gff()
with open(snpwork_genomes/(self.name+'.fa'),'wb') as f:
for name, seq in io.read_sequences(self.reference_fasta_filename()):
io.write_fasta(f, name, seq)
io.execute('java -jar JAR build NAME -gff3 -c CONFIG',
JAR=jar, NAME=self.name, CONFIG=self/'snpeff.config')
def run(self):
assert self.sort in ('queryname', 'coordinate')
jar = io.find_jar('MergeSamFiles.jar', 'MergeSamFiles is part of the Picard package.')
io.execute([
'java','-jar',jar,
'USE_THREADING=true',
'TMP_DIR='+tempfile.gettempdir(), #Force picard to use same temp dir as Python
'SORT_ORDER='+self.sort,
'OUTPUT='+self.prefix+'.bam'
] + [ 'INPUT='+item for item in self.bams ])
if self.sort == 'coordinate' and self.index:
jar = io.find_jar('BuildBamIndex.jar', 'BuildBamIndex is part of the Picard package.')
io.execute([
'java','-jar',jar,
'INPUT='+self.prefix+'.bam'
])
def run(self):
assert self.sort in ('queryname', 'coordinate')
jar = io.find_jar('MergeSamFiles.jar', 'MergeSamFiles is part of the Picard package.')
io.execute([
'java','-jar',jar,
'USE_THREADING=true',
'TMP_DIR='+tempfile.gettempdir(), #Force picard to use same temp dir as Python
'SORT_ORDER='+self.sort,
'OUTPUT='+self.prefix+'.bam'
] + [ 'INPUT='+item for item in self.bams ])
if self.sort == 'coordinate' and self.index:
jar = io.find_jar('BuildBamIndex.jar', 'BuildBamIndex is part of the Picard package.')
io.execute([
'java','-jar',jar,
'INPUT='+self.prefix+'.bam'
])
def run(self):
with workspace.tempspace() as temp:
with open(temp/'batch.txt','wb') as f:
print >> f, 'new'
print >> f, 'genome '+os.path.abspath(self.genome)
for filename in self.files:
print >> f, 'load '+os.path.abspath(filename)
io.execute(['java','-jar',io.find_jar('igv.jar'),'-b',temp/'batch.txt'])
def run(self):
reference = reference_directory.Reference(self.reference, must_exist=True)
jar = io.find_jar('snpEff.jar')
with open(self.prefix + '.vcf','wb') as f:
io.execute('java -jar JAR eff GENOME VCF -c CONFIG',
JAR=jar, GENOME=reference.name, VCF=self.vcf, CONFIG=reference/'snpeff.config',
stdout=f)
index_vcf(self.prefix+'.vcf')
def run(self):
with workspace.tempspace() as temp:
with open(temp/'batch.txt','wb') as f:
print >> f, 'new'
print >> f, 'preference LAST_TRACK_DIRECTORY', os.getcwd()
print >> f, 'preference LAST_GENOME_IMPORT_DIRECTORY', os.getcwd()
print >> f, 'genome '+os.path.abspath(self.genome)
for filename in self.files:
print >> f, 'load '+os.path.abspath(filename)
io.execute(['java','-jar',io.find_jar('igv.jar'),'-b',temp/'batch.txt'])
def run(self):
reference = reference_directory.Reference(self.reference,
must_exist=True)
jar = io.find_jar('snpEff.jar')
with open(self.prefix + '.vcf', 'wb') as f:
io.execute('java -jar JAR eff GENOME VCF -c CONFIG',
JAR=jar,
GENOME=reference.name,
VCF=self.vcf,
CONFIG=reference / 'snpeff.config',
stdout=f)
index_vcf(self.prefix + '.vcf')