def run(self):
sequences = [ ]
annotations = [ ]
for filename in self.filenames:
any = False
if io.is_sequence_file(filename):
sequences.append(filename)
any = True
if annotation.is_annotation_file(filename):
annotations.append(filename)
any = True
if not any:
raise grace.Error(filename + ' is neither a sequence file nor an annotation file that nesoni can read.')
if not sequences:
assert not annotations, 'Annotations given without any reference sequences.'
reference = Reference(self.output_dir, must_exist=True)
else:
reference = Reference(self.output_dir, must_exist=False)
reference.set_sequences(sequences)
reference.set_annotations(annotations)
with legion.Stage() as stage:
if self.genome:
stage.process(reference.build_genome, self.genome_select)
if config.apply_ifavailable_program(self.bowtie, 'bowtie2-build'):
stage.process(reference.build_bowtie_index)
if config.apply_ifavailable_program(self.ls, 'gmapper-ls'):
stage.process(reference.build_shrimp_mmap, False)
if config.apply_ifavailable_program(self.cs, 'gmapper-cs'):
stage.process(reference.build_shrimp_mmap, True)
if config.apply_ifavailable_jar(self.snpeff, 'snpEff.jar'):
stage.process(reference.build_snpeff)
def run(self):
sequences = [ ]
annotations = [ ]
for filename in self.filenames:
any = False
if io.is_sequence_file(filename):
sequences.append(filename)
any = True
if annotation.is_annotation_file(filename):
annotations.append(filename)
any = True
if not any:
raise grace.Error(filename + ' is neither a sequence file nor an annotation file that nesoni can read.')
if not sequences:
assert not annotations, 'Annotations given without any reference sequences.'
reference = Reference(self.output_dir, must_exist=True)
else:
reference = Reference(self.output_dir, must_exist=False)
reference.set_sequences(sequences)
reference.set_annotations(annotations)
with open(self.log_filename(),'wb') as f:
if self.ls:
reference.build_shrimp_mmap(False, f)
if self.cs:
reference.build_shrimp_mmap(True, f)
if self.bowtie:
reference.build_bowtie_index(f)
if self.genome:
reference.build_genome(self.genome_select)
if self.snpeff:
reference.build_snpeff()
def run(self):
base = os.path.split(self.prefix)[1]
annotations = [ ]
sequences = [ ]
for filename in self.filenames:
any = False
if io.is_sequence_file(filename):
sequences.append(filename)
any = True
if annotation.is_annotation_file(filename):
annotations.append(filename)
any = True
assert any, 'File is neither a recognized sequence or annotation file'
cytoband_filename = os.path.join(self.prefix,base+'_cytoband.txt')
property_filename = os.path.join(self.prefix,'property.txt')
gff_filename = os.path.join(self.prefix,base+'.gff')
output_filenames = [ cytoband_filename, property_filename, gff_filename ]
if not os.path.exists(self.prefix):
os.mkdir(self.prefix)
f = open(property_filename,'wb')
print >> f, 'ordered=true'
print >> f, 'id=%s' % base
print >> f, 'name=%s' % (self.name or base)
print >> f, 'cytobandFile=%s_cytoband.txt' % base
print >> f, 'geneFile=%s.gff' % base
print >> f, 'sequenceLocation=%s' % base
f.close()
trivia.As_gff(output=gff_filename,
filenames=annotations,
exclude=[ 'gene', 'source' ]
).run()
f_cyt = open(cytoband_filename,'wb')
for filename in sequences:
for name, seq in io.read_sequences(filename):
assert '/' not in name
f = open(os.path.join(self.prefix, name + '.txt'), 'wb')
f.write(seq)
f.close()
print >> f_cyt, '%s\t0\t%d' % (name, len(seq))
f_cyt.close()
genome_filename = self.prefix + '.genome'
if os.path.exists(genome_filename):
os.unlink(genome_filename)
io.execute(
['zip', '-j', io.abspath(genome_filename)] +
[ io.abspath(item) for item in output_filenames ]
)
for filename in output_filenames:
if os.path.exists(filename):
os.unlink(filename)
def run(self):
sequences = [ ]
annotations = [ ]
for filename in self.filenames:
any = False
if io.is_sequence_file(filename):
sequences.append(filename)
any = True
if annotation.is_annotation_file(filename):
annotations.append(filename)
any = True
if not any:
raise grace.Error(filename + ' is neither a sequence file nor an annotation file that nesoni can read.')
reference = Reference(self.output_dir, must_exist=False)
reference.set_sequences(sequences)
reference.set_annotations(annotations)
if self.ls:
reference.build_shrimp_mmap(False)
if self.cs:
reference.build_shrimp_mmap(True)
def run(self):
sequences = []
annotations = []
for filename in self.filenames:
any = False
if io.is_sequence_file(filename):
sequences.append(filename)
any = True
if annotation.is_annotation_file(filename):
annotations.append(filename)
any = True
if not any:
raise grace.Error(
filename +
' is neither a sequence file nor an annotation file that nesoni can read.'
)
reference = Reference(self.output_dir, must_exist=False)
reference.set_sequences(sequences)
reference.set_annotations(annotations)
if self.ls:
reference.build_shrimp_mmap(False)
if self.cs:
reference.build_shrimp_mmap(True)
def run(self):
bams = [ ]
reference = None
reference2 = None
extra = [ ]
for sample in self.samples:
if sam.is_bam(sample):
bams.append(sample)
elif os.path.isdir(sample):
working = working_directory.Working(sample,True)
bams.append( working.get_filtered_sorted_bam() )
extra.append( '##sampleTags=' + ','.join(working.get_tags()) )
if reference2 is None:
reference2 = working.get_reference().reference_fasta_filename()
elif io.is_sequence_file(sample):
assert reference is None, 'Only one reference FASTA file allowed.'
reference = sample
if reference is None:
reference = reference2
if reference is None:
raise grace.Error('No reference FASTA file given.')
with nesoni.Stage() as stage:
tempspace = stage.enter( workspace.tempspace() )
if self.depth_limit:
with nesoni.Stage() as stage2:
for i in xrange(len(bams)):
sam.Bam_depth_limit(
tempspace/('%d'%i),
bams[i],
depth=self.depth_limit
).process_make(stage2)
bams[i] = tempspace/('%d.bam'%i)
# FreeBayes claims to handle multiple bams, but it doesn't actually work
if len(bams) > 1:
sam.Bam_merge(tempspace/'merged', bams=bams, index=False).run()
bams = [ tempspace/'merged.bam' ]
command = [
'freebayes',
'-f', reference,
'--ploidy',str(self.ploidy),
'--pvar',str(self.pvar),
] + self.freebayes_options + bams
self.log.log('Running: '+' '.join(command)+'\n')
f_out = stage.enter( open(self.prefix+'.vcf','wb') )
f_in = stage.enter( io.pipe_from(command) )
done_extra = False
for line in f_in:
if not done_extra and not line.startswith('##'):
for extra_line in extra:
f_out.write(extra_line+'\n')
done_extra = True
f_out.write(line)
index_vcf(self.prefix+'.vcf')
def run(self):
bams = []
reference = None
reference2 = None
extra = []
for sample in self.samples:
if sam.is_bam(sample):
bams.append(sample)
elif os.path.isdir(sample):
working = working_directory.Working(sample, True)
bams.append(working.get_filtered_sorted_bam())
extra.append('##sampleTags=' + ','.join(working.get_tags()))
if reference2 is None:
reference2 = working.get_reference(
).reference_fasta_filename()
elif io.is_sequence_file(sample):
assert reference is None, 'Only one reference FASTA file allowed.'
reference = sample
if reference is None:
reference = reference2
if reference is None:
raise grace.Error('No reference FASTA file given.')
with nesoni.Stage() as stage:
tempspace = stage.enter(workspace.tempspace())
if self.depth_limit:
with nesoni.Stage() as stage2:
for i in xrange(len(bams)):
sam.Bam_depth_limit(
tempspace / ('%d' % i),
bams[i],
depth=self.depth_limit).process_make(stage2)
bams[i] = tempspace / ('%d.bam' % i)
# FreeBayes claims to handle multiple bams, but it doesn't actually work
if len(bams) > 1:
sam.Bam_merge(tempspace / 'merged', bams=bams,
index=False).run()
bams = [tempspace / 'merged.bam']
command = [
'freebayes',
'-f',
reference,
'--ploidy',
str(self.ploidy),
'--pvar',
str(self.pvar),
] + self.freebayes_options + bams
self.log.log('Running: ' + ' '.join(command) + '\n')
f_out = stage.enter(open(self.prefix + '.vcf', 'wb'))
f_in = stage.enter(io.pipe_from(command))
done_extra = False
for line in f_in:
if not done_extra and not line.startswith('##'):
for extra_line in extra:
f_out.write(extra_line + '\n')
done_extra = True
f_out.write(line)
index_vcf(self.prefix + '.vcf')